diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index 5f3a67b4b..4cf30ab1c 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 22 18:31:24 2024Sun Sep 15 18:32:12 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 23 06:26:44 2024Mon Sep 16 06:27:02 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 9e9b92b53..645785024 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -84,11 +84,11 @@ "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", - "date1": "Mon Sep 16 06:27:02 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-16-06-12-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-09-06-11-1/results.html", - "date2": "Mon Sep 09 06:26:24 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/results.html", + "date1": "Mon Sep 23 06:26:44 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/tools.yml", + "run2": "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", + "date2": "Mon Sep 16 06:27:02 2024" }, "11": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-21-18-15-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/chunk.json new file mode 100644 index 000000000..825526e60 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/chunk.json @@ -0,0 +1,7 @@ +{ + "0": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/results.html", + "date1": "Mon Sep 23 06:26:44 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/chunk.txt new file mode 100644 index 000000000..62914ed92 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/chunk.txt @@ -0,0 +1,25 @@ +-t unicycler --tool-version 9e3e80cc4ad4 +-t deeptools_bam_compare --tool-version e821645ef8fc +-t cutadapt --tool-version 093678460093 +-t cutadapt --tool-version 135b80fb1ac2 +-t fastqc --tool-version 3d0c7bdf12f5 +-t fastqc --tool-version e7b2202befea +-t rna_starsolo --tool-version eec9494fdafa +-t rna_starsolo --tool-version 79b885ce78d7 +-t poretools_hist --tool-version 5a82eb9e1b89 +-t picard --tool-version b502c227b5e6 +-t samtools_view --tool-version b72793637686 +-t samtools_split --tool-version 135c85f4cfaf +-t sam_merge --tool-version 1977f1637890 +-t dropletutils_read_10x --tool-version ca62f52e0d7f +-t scater_normalize --tool-version 946179ef029c +-t anndata_ops --tool-version 54f1212d26ac +-t anndata_ops --tool-version 6aa025ea64d3 +-t scanpy_plot_embed --tool-version 99dd7baf9e23 +-t scanpy_plot_embed --tool-version a8ef4bc35839 +-t jq --tool-version 5ff75eb1a893 +-t snpsift_dbnsfp --tool-version 4e21e4f2bc48 +-t bcftools_plugin_counts --tool-version 4813f99d81b7 +-t bcftools_view --tool-version 23680a42e149 +-t vcfcheck --tool-version 2968c6916579 +-t vcfdistance --tool-version 5822b40f3037 diff --git a/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/012ff491024a103d.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/012ff491024a103d.json new file mode 100644 index 000000000..f5018be70 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/012ff491024a103d.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "012ff491024a103d", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T06:41:22.713459", + "update_time": "2024-09-23T06:41:33.505423", + "galaxy_version": "24.1", + "external_id": "gxy-grx9c", + "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' '68:/galaxy/server/database/objects/b/c/4/dataset_bc491a7e-04ba-4d27-bcfe-54610f49ac97_files:/galaxy/server/database/objects/b/c/4/dataset_bc491a7e-04ba-4d27-bcfe-54610f49ac97.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_rn6k7235\"", + "files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bwa-mem-fastq2_assimetric.fq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9p8htxjc\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastq.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "29192b1e2b9e7b20", + "src": "hda", + "uuid": "bc491a7e-04ba-4d27-bcfe-54610f49ac97" + } + }, + "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-24-09-23-06-12-1/errors/242180e9e118d62b.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/242180e9e118d62b.json new file mode 100644 index 000000000..5af0889ac --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/242180e9e118d62b.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "242180e9e118d62b", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:12:51.835349", + "update_time": "2024-09-23T07:13:02.395004", + "galaxy_version": "24.1", + "external_id": "gxy-5zfnd", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/185/registry.xml' '/galaxy/server/database/jobs_directory/000/185/upload_params.json' '229:/galaxy/server/database/objects/9/1/4/dataset_9140b870-5465-4a80-bfe5-ce4bd8c09c09_files:/galaxy/server/database/objects/9/1/4/dataset_9140b870-5465-4a80-bfe5-ce4bd8c09c09.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_2zrsc793\"", + "files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bwa-mem-fastq1.fq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_z6i5pmcl\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastq.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "121d75de73994175", + "src": "hda", + "uuid": "9140b870-5465-4a80-bfe5-ce4bd8c09c09" + } + }, + "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-24-09-23-06-12-1/errors/33349d9168d83366.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/33349d9168d83366.json new file mode 100644 index 000000000..4d3e0296e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/33349d9168d83366.json @@ -0,0 +1,52 @@ +{ + "model_class": "Job", + "id": "33349d9168d83366", + "history_id": "abbc0a781ea0cf97", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T08:13:56.431831", + "update_time": "2024-09-23T08:14:01.873314", + "galaxy_version": "24.1", + "external_id": "gxy-xp65v", + "handler": null, + "job_runner_name": null, + "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/2/a/d/dataset_2ad787a9-2083-4145-8593-16b90dd28f85.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --samples 'NA00002' --min-ac 1 --max-ac 1 --types \"snps\" --regions-overlap 1 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/0/c/8/dataset_0c86100c-0640-493b-9cc3-1b2080b9b4cc.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": null, \"invert_targets_file\": false}", + "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": null, \"max_ac\": \"1\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"1\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": null, \"private\": null, \"select_genotype\": null, \"types\": \"snps\", \"uncalled\": null}", + "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"NA00002\", \"samples_file\": null, \"trim_alt_alleles\": false}", + "sec_restrict": "{\"apply_filters\": \"\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}" + }, + "inputs": { + "input_file": { + "id": "0aff707637dcc57b", + "src": "hda", + "uuid": "2ad787a9-2083-4145-8593-16b90dd28f85" + } + }, + "outputs": { + "output_file": { + "id": "10723048ea900c78", + "src": "hda", + "uuid": "0c86100c-0640-493b-9cc3-1b2080b9b4cc" + } + }, + "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-24-09-23-06-12-1/errors/363809241d2e2d64.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/363809241d2e2d64.json new file mode 100644 index 000000000..a5033434d --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/363809241d2e2d64.json @@ -0,0 +1,49 @@ +{ + "model_class": "Job", + "id": "363809241d2e2d64", + "history_id": "abbc0a781ea0cf97", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:59:50.616480", + "update_time": "2024-09-23T07:59:55.788130", + "galaxy_version": "24.1", + "external_id": "gxy-bvgp9", + "handler": null, + "job_runner_name": null, + "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/4/d/2/dataset_4d2d6f9a-a69a-442d-922d-4a8a589f2557.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/20; print(frac > 1 ? 6776+1/frac : \".0\")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"sam\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", + "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"\", \"select_subsample\": \"target\", \"target\": \"20\"}}}" + }, + "inputs": { + "input": { + "id": "9ba29b32212e9193", + "src": "hda", + "uuid": "4d2d6f9a-a69a-442d-922d-4a8a589f2557" + } + }, + "outputs": { + "outputsam": { + "id": "8e06e5b36898b515", + "src": "hda", + "uuid": "64ee866e-0707-46e5-bd5b-73a833baf83c" + } + }, + "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-24-09-23-06-12-1/errors/49adb5f856bc6730.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/49adb5f856bc6730.json new file mode 100644 index 000000000..bb70804bb --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/49adb5f856bc6730.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "49adb5f856bc6730", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:21:39.458280", + "update_time": "2024-09-23T07:21:50.363149", + "galaxy_version": "24.1", + "external_id": "gxy-dcw7t", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/221/registry.xml' '/galaxy/server/database/jobs_directory/000/221/upload_params.json' '273:/galaxy/server/database/objects/4/6/f/dataset_46fbbabd-90ea-4e08-b61a-98b91c9795be_files:/galaxy/server/database/objects/4/6/f/dataset_46fbbabd-90ea-4e08-b61a-98b91c9795be.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_a1fmm3f4\"", + "files_metadata": "{\"__current_case__\": 78, \"file_type\": \"fastq\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"1000trimmed.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_rghzxhre\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastq\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "7ab67487331b1c1a", + "src": "hda", + "uuid": "46fbbabd-90ea-4e08-b61a-98b91c9795be" + } + }, + "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-24-09-23-06-12-1/errors/56d12ec3242f54cb.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/56d12ec3242f54cb.json new file mode 100644 index 000000000..387ac1dc4 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/56d12ec3242f54cb.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "56d12ec3242f54cb", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:12:05.082288", + "update_time": "2024-09-23T07:12:16.197787", + "galaxy_version": "24.1", + "external_id": "gxy-q7vl6", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/180/registry.xml' '/galaxy/server/database/jobs_directory/000/180/upload_params.json' '223:/galaxy/server/database/objects/5/1/1/dataset_5114b8d1-d54c-4111-b7be-20805fd54b4d_files:/galaxy/server/database/objects/5/1/1/dataset_5114b8d1-d54c-4111-b7be-20805fd54b4d.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_awrq_0q9\"", + "files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bwa-mem-fastq1_assimetric.fq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_57rcuy04\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastq.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "2f502f8caf6f5267", + "src": "hda", + "uuid": "5114b8d1-d54c-4111-b7be-20805fd54b4d" + } + }, + "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-24-09-23-06-12-1/errors/5b2bf096077bd243.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/5b2bf096077bd243.json new file mode 100644 index 000000000..aafffa4cb --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/5b2bf096077bd243.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "5b2bf096077bd243", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": 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\"file_data\": \"/galaxy/server/database/tmp/upload_file_data_tmvvsbrb\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "a2c05ef4a0017263", + "src": "hda", + "uuid": "71722d05-4f44-4443-9471-d1210ff8a7ad" + } + }, + "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-24-09-23-06-12-1/errors/6465231d7923c4e0.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/6465231d7923c4e0.json new file mode 100644 index 000000000..cf90e3a9b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/6465231d7923c4e0.json @@ 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b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/6fa2df4c710d9e61.json new file mode 100644 index 000000000..a187fdc32 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/6fa2df4c710d9e61.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "6fa2df4c710d9e61", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:32:43.079302", + "update_time": "2024-09-23T07:32:54.351547", + "galaxy_version": "24.1", + "external_id": "gxy-dwgmr", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/270/registry.xml' '/galaxy/server/database/jobs_directory/000/270/upload_params.json' '345:/galaxy/server/database/objects/4/b/f/dataset_4bf45bbd-0385-4ef6-9ada-b5c11e69be63_files:/galaxy/server/database/objects/4/b/f/dataset_4bf45bbd-0385-4ef6-9ada-b5c11e69be63.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_6da60i2j\"", + "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"pbmc_1k_v2_L001.R2.10k.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ix3y77cu\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "c2e5a7224130b76a", + "src": "hda", + "uuid": "4bf45bbd-0385-4ef6-9ada-b5c11e69be63" + } + }, + "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-24-09-23-06-12-1/errors/7832d5e7f2f81f0f.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/7832d5e7f2f81f0f.json new file mode 100644 index 000000000..0fb5795b6 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/7832d5e7f2f81f0f.json @@ -0,0 +1,52 @@ +{ + "model_class": "Job", + "id": "7832d5e7f2f81f0f", + "history_id": "abbc0a781ea0cf97", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:47:10.920996", + "update_time": "2024-09-23T07:47:17.971108", + "galaxy_version": "24.1", + "external_id": "gxy-jgw5b", + "handler": null, + "job_runner_name": null, + "command_line": "export MPLBACKEND=\"agg\" && poretools hist '/galaxy/server/database/objects/0/c/b/dataset_0cbaba6f-e05d-46fe-93ef-ef71c3963030.dat' --saveas histogram.pdf --min-length 0 --max-length 1000000000 --num-bins 50 && mv histogram.pdf '/galaxy/server/database/objects/3/9/6/dataset_3969aa18-80bc-4c7c-b233-20dd75902089.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fast5.tar\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "num_bins": "\"50\"", + "max_length": "\"1000000000\"", + "min_length": "\"0\"", + "theme_bw": "false", + "extension": "\"pdf\"" + }, + "inputs": { + "input": { + "id": "fca5fc051c4ad73e", + "src": "hda", + "uuid": "0cbaba6f-e05d-46fe-93ef-ef71c3963030" + } + }, + "outputs": { + "output": { + "id": "1911e35313353edc", + "src": "hda", + "uuid": "3969aa18-80bc-4c7c-b233-20dd75902089" + } + }, + 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"model_class": "Job", + "id": "8b10689ed5d7ab17", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:39:13.021822", + "update_time": "2024-09-23T07:39:31.210231", + "galaxy_version": "24.1", + "external_id": "gxy-9ttk7", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/326/registry.xml' '/galaxy/server/database/jobs_directory/000/326/upload_params.json' '416:/galaxy/server/database/objects/e/d/f/dataset_edff5ec5-749a-4392-bd45-b418e1a84d86_files:/galaxy/server/database/objects/e/d/f/dataset_edff5ec5-749a-4392-bd45-b418e1a84d86.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_mxv5fhm3\"", + "files_metadata": "{\"__current_case__\": 105, \"file_type\": \"gtf\"}", + "dbkey": 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b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/8c3d34315d165182.json new file mode 100644 index 000000000..3c7054de4 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/8c3d34315d165182.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "8c3d34315d165182", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:36:06.621302", + "update_time": "2024-09-23T07:37:29.702873", + "galaxy_version": "24.1", + "external_id": "gxy-6jxvv", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/298/registry.xml' '/galaxy/server/database/jobs_directory/000/298/upload_params.json' '383:/galaxy/server/database/objects/1/d/a/dataset_1da881b0-5a81-4ed6-8278-3ccd5f9b6213_files:/galaxy/server/database/objects/1/d/a/dataset_1da881b0-5a81-4ed6-8278-3ccd5f9b6213.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_0n8sily9\"", + "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"smartseq3.R1.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_5zrkoseb\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "125fec9e442388a1", + "src": "hda", + "uuid": "1da881b0-5a81-4ed6-8278-3ccd5f9b6213" + } + }, + "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-24-09-23-06-12-1/errors/9793c3ab30596a97.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/9793c3ab30596a97.json new file mode 100644 index 000000000..d5479af3e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/9793c3ab30596a97.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "9793c3ab30596a97", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:27:17.667879", + "update_time": "2024-09-23T07:27:28.784782", + "galaxy_version": "24.1", + "external_id": "gxy-vx85f", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/245/registry.xml' '/galaxy/server/database/jobs_directory/000/245/upload_params.json' '305:/galaxy/server/database/objects/2/0/b/dataset_20bd3261-ac9c-4fe8-82ec-fbae879975cc_files:/galaxy/server/database/objects/2/0/b/dataset_20bd3261-ac9c-4fe8-82ec-fbae879975cc.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_ehgv4je6\"", + "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"hisat_output_1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_5d60_6or\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"bam\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "d0b5b8ece218a103", + "src": "hda", + "uuid": "20bd3261-ac9c-4fe8-82ec-fbae879975cc" + } + }, + "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-24-09-23-06-12-1/errors/99f8cf4b9e420d72.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/99f8cf4b9e420d72.json new file mode 100644 index 000000000..09b1b7641 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/99f8cf4b9e420d72.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "99f8cf4b9e420d72", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:44:30.604265", + "update_time": "2024-09-23T07:45:49.417655", + "galaxy_version": "24.1", + "external_id": "gxy-mpzx2", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/376/registry.xml' '/galaxy/server/database/jobs_directory/000/376/upload_params.json' '481:/galaxy/server/database/objects/4/d/a/dataset_4dabdc65-e4a9-40fc-8af4-5a7e1e59f60f_files:/galaxy/server/database/objects/4/d/a/dataset_4dabdc65-e4a9-40fc-8af4-5a7e1e59f60f.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_x4dgzffp\"", + "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"smartseq9.R2.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_uz2hn1o1\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "4d48f5e1b172e8fb", + "src": "hda", + "uuid": "4dabdc65-e4a9-40fc-8af4-5a7e1e59f60f" + } + }, + "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-24-09-23-06-12-1/errors/a2e8b7e2af2b45b2.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/a2e8b7e2af2b45b2.json new file mode 100644 index 000000000..803533017 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/a2e8b7e2af2b45b2.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "a2e8b7e2af2b45b2", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T06:59:56.906114", + "update_time": "2024-09-23T07:00:09.342972", + "galaxy_version": "24.1", + "external_id": "gxy-w4kzv", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/131/registry.xml' '/galaxy/server/database/jobs_directory/000/131/upload_params.json' '165:/galaxy/server/database/objects/5/7/3/dataset_573471fd-40a9-4259-bfa4-0af6c40fcee8_files:/galaxy/server/database/objects/5/7/3/dataset_573471fd-40a9-4259-bfa4-0af6c40fcee8.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_44oirvnw\"", + "files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"cutadapt_in_split.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_8oi_8soz\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastq.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "0f3aaf74d6fd278f", + "src": "hda", + "uuid": "573471fd-40a9-4259-bfa4-0af6c40fcee8" + } + }, + "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-24-09-23-06-12-1/errors/c01ea000a8fa16a6.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/c01ea000a8fa16a6.json new file mode 100644 index 000000000..83dec63a5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/c01ea000a8fa16a6.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "c01ea000a8fa16a6", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T06:31:45.261260", + "update_time": "2024-09-23T06:31:55.497539", + "galaxy_version": "24.1", + "external_id": "gxy-5ls67", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/15/registry.xml' '/galaxy/server/database/jobs_directory/000/15/upload_params.json' '17:/galaxy/server/database/objects/d/3/7/dataset_d3782a0e-1153-4557-8db0-be6481f629c9_files:/galaxy/server/database/objects/d/3/7/dataset_d3782a0e-1153-4557-8db0-be6481f629c9.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_i15f0zjw\"", + "files_metadata": "{\"__current_case__\": 78, \"file_type\": \"fastq\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"cutadapt_small.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_2flq_pbm\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastq\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "c17966a0831dcc16", + "src": "hda", + "uuid": "d3782a0e-1153-4557-8db0-be6481f629c9" + } + }, + "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-24-09-23-06-12-1/errors/c7325399e5e03695.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/c7325399e5e03695.json new file mode 100644 index 000000000..0d13a45aa --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/c7325399e5e03695.json @@ -0,0 +1,52 @@ +{ + "model_class": "Job", + "id": "c7325399e5e03695", + "history_id": "abbc0a781ea0cf97", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T08:08:59.976222", + "update_time": "2024-09-23T08:09:05.832815", + "galaxy_version": "24.1", + "external_id": "gxy-fn6n2", + "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/5/0/dataset_f50aa6f4-2f8b-4202-af6b-13b19268d92f.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --samples 'NA00003' --known --exclude-private --apply-filters 'PASS' --regions 'Y:20-' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/a/9/0/dataset_a90606f7-504f-4563-b5b8-d11e15c5e392.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": null, \"invert_targets_file\": false}", + "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": \"--known\", \"max_ac\": \"\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": null, \"private\": \"--exclude-private\", \"select_genotype\": null, \"types\": null, \"uncalled\": null}", + "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"NA00003\", \"samples_file\": null, \"trim_alt_alleles\": false}", + "sec_restrict": "{\"apply_filters\": \"PASS\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 1, \"regions\": [{\"__index__\": 0, \"chrom\": \"Y\", \"start\": \"20\", \"stop\": null}], \"regions_src\": \"regions\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}" + }, + "inputs": { + "input_file": { + "id": "4d6697a390ab2b7e", + "src": "hda", + "uuid": "f50aa6f4-2f8b-4202-af6b-13b19268d92f" + } + }, + "outputs": { + "output_file": { + "id": "ae59338e30d2df3a", + "src": "hda", + "uuid": "a90606f7-504f-4563-b5b8-d11e15c5e392" + } + }, + "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-24-09-23-06-12-1/errors/c78b432e4d833a49.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/c78b432e4d833a49.json new file mode 100644 index 000000000..70a0e6022 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/c78b432e4d833a49.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "c78b432e4d833a49", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:36:08.652487", + "update_time": "2024-09-23T07:37:30.319444", + "galaxy_version": "24.1", + "external_id": "gxy-w72jp", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/303/registry.xml' '/galaxy/server/database/jobs_directory/000/303/upload_params.json' '388:/galaxy/server/database/objects/c/b/3/dataset_cb3f60f5-6125-43a2-bdd6-b9704c471714_files:/galaxy/server/database/objects/c/b/3/dataset_cb3f60f5-6125-43a2-bdd6-b9704c471714.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_atfrilxf\"", + "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"smartseq5.R2.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_vtsgh5wt\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "c0234df653c5db45", + "src": "hda", + "uuid": "cb3f60f5-6125-43a2-bdd6-b9704c471714" + } + }, + "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-24-09-23-06-12-1/errors/d34d62e91a86c784.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/d34d62e91a86c784.json new file mode 100644 index 000000000..c702c103e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/d34d62e91a86c784.json @@ -0,0 +1,63 @@ +{ + "model_class": "Job", + "id": "d34d62e91a86c784", + "history_id": "abbc0a781ea0cf97", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T06:34:02.635518", + "update_time": "2024-09-23T06:34:07.056899", + "galaxy_version": "24.1", + "external_id": "gxy-rbhsm", + "handler": null, + "job_runner_name": null, + "command_line": "ln -f -s '/galaxy/server/database/objects/5/7/b/dataset_57b443b6-2449-4c1e-940d-705244af818a.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --info-file='/galaxy/server/database/objects/3/8/9/dataset_389b778e-00bb-4d28-b79a-c44c182d94db.dat' -o 'out1.fq' 'cutadapt_small_fastq.fq' > report.txt", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_selector": "[\"report\", \"info_file\"]", + "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", + "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", + "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", + "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", + "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 28, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}" + }, + "inputs": { + "library|input_1": { + "id": "a6dc655213a10cb8", + "src": "hda", + "uuid": "57b443b6-2449-4c1e-940d-705244af818a" + } + }, + "outputs": { + "info_file": { + "id": "df0cf971a23d18a1", + "src": "hda", + "uuid": "389b778e-00bb-4d28-b79a-c44c182d94db" + }, + "report": { + "id": "a9473ff78ba6571a", + "src": "hda", + "uuid": "8ff16f52-2b79-446d-a011-55c20adfe29e" + }, + "out1": { + "id": "02ee2ca586d13cce", + "src": "hda", + "uuid": "6412f1a4-e291-47df-932e-bcb2c7d47fe1" + } + }, + "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-24-09-23-06-12-1/errors/d9aac45ce2572489.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/d9aac45ce2572489.json new file mode 100644 index 000000000..6c96de560 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/d9aac45ce2572489.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "d9aac45ce2572489", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:59:56.593692", + "update_time": "2024-09-23T08:00:09.584233", + "galaxy_version": "24.1", + "external_id": "gxy-sk96x", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/434/registry.xml' '/galaxy/server/database/jobs_directory/000/434/upload_params.json' '539:/galaxy/server/database/objects/7/a/6/dataset_7a6b55f3-1d00-40dc-b24e-90484da932fb_files:/galaxy/server/database/objects/7/a/6/dataset_7a6b55f3-1d00-40dc-b24e-90484da932fb.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_wl4fiw4h\"", + "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"no_reads.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_d9m3i8zd\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"bam\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "af637ce7dd7ebd35", + "src": "hda", + "uuid": "7a6b55f3-1d00-40dc-b24e-90484da932fb" + } + }, + "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-24-09-23-06-12-1/errors/da29229986daa3b5.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/da29229986daa3b5.json new file mode 100644 index 000000000..5ecf759c3 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/da29229986daa3b5.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "da29229986daa3b5", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:13:38.079366", + "update_time": "2024-09-23T07:13:48.539885", + "galaxy_version": "24.1", + "external_id": "gxy-d9x6f", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/190/registry.xml' '/galaxy/server/database/jobs_directory/000/190/upload_params.json' '235:/galaxy/server/database/objects/9/e/b/dataset_9eb12ed8-a952-4464-9245-200fcff49cb4_files:/galaxy/server/database/objects/9/e/b/dataset_9eb12ed8-a952-4464-9245-200fcff49cb4.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_c6qskmt4\"", + "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"polya.1.fasta\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ktmv2shp\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fasta\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "cf9e963df952ec5d", + "src": "hda", + "uuid": "9eb12ed8-a952-4464-9245-200fcff49cb4" + } + }, + "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-24-09-23-06-12-1/errors/dd08e6354119fae5.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/dd08e6354119fae5.json new file mode 100644 index 000000000..fae92aae7 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/dd08e6354119fae5.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "dd08e6354119fae5", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:33:11.596708", + "update_time": "2024-09-23T07:33:23.210311", + "galaxy_version": "24.1", + "external_id": "gxy-dcm8l", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/272/registry.xml' '/galaxy/server/database/jobs_directory/000/272/upload_params.json' '347:/galaxy/server/database/objects/e/c/1/dataset_ec1b62c6-fd6b-48d4-9a58-7eecc7974d7c_files:/galaxy/server/database/objects/e/c/1/dataset_ec1b62c6-fd6b-48d4-9a58-7eecc7974d7c.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_w9qcv3lw\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_anjz_fvd\", \"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": "b83a94cb295b94cc", + "src": "hda", + "uuid": "ec1b62c6-fd6b-48d4-9a58-7eecc7974d7c" + } + }, + "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-24-09-23-06-12-1/errors/e0074b11b028094a.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/e0074b11b028094a.json new file mode 100644 index 000000000..827ffc4e7 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/e0074b11b028094a.json @@ -0,0 +1,58 @@ +{ + "model_class": "Job", + "id": "e0074b11b028094a", + "history_id": "abbc0a781ea0cf97", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:01:03.523812", + "update_time": "2024-09-23T07:01:09.297845", + "galaxy_version": "24.1", + "external_id": "gxy-bvvzs", + "handler": null, + "job_runner_name": null, + "command_line": "ln -f -s '/galaxy/server/database/objects/d/5/f/dataset_d5fec4af-476b-41f1-9fcb-e9ac5aa7e8f5.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output='untrimmed_output.fq.gz' -o 'out1.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_selector": "\"untrimmed_file\"", + "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", + "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", + "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", + "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", + "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 170, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}" + }, + "inputs": { + "library|input_1": { + "id": "0308fa1b7d867675", + "src": "hda", + "uuid": "d5fec4af-476b-41f1-9fcb-e9ac5aa7e8f5" + } + }, + "outputs": { + "untrimmed_output": { + "id": "2b949ef2f85af451", + "src": "hda", + "uuid": "542390ae-1de7-49f4-965a-7e19634c592c" + }, + "out1": { + "id": "6cf4c296eae030fb", + "src": "hda", + "uuid": "85a2ecec-c245-4fa1-8f39-fb04c1d3fe04" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output=untrimmed_output.fq.gz -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.159 s (1601.046 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 2 (2.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (2.0%)\n\nTotal basepairs processed: 24,849 bp\nTotal written (filtered): 496 bp (2.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output=untrimmed_output.fq.gz -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.159 s (1601.046 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 2 (2.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (2.0%)\n\nTotal basepairs processed: 24,849 bp\nTotal written (filtered): 496 bp (2.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/e3e7a4141b23f3d4.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/e3e7a4141b23f3d4.json new file mode 100644 index 000000000..60ae8d3b0 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/e3e7a4141b23f3d4.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "e3e7a4141b23f3d4", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:43:54.893827", + "update_time": "2024-09-23T07:44:06.020420", + "galaxy_version": "24.1", + "external_id": "gxy-49wcv", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/352/registry.xml' '/galaxy/server/database/jobs_directory/000/352/upload_params.json' '457:/galaxy/server/database/objects/6/f/8/dataset_6f8b6e2c-3488-4f01-a1df-84612e210d46_files:/galaxy/server/database/objects/6/f/8/dataset_6f8b6e2c-3488-4f01-a1df-84612e210d46.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_de2zkaiv\"", + "files_metadata": "{\"__current_case__\": 105, \"file_type\": \"gtf\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"filtered3.Homo_sapiens.GRCh38.100.chr21.gtf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_i7riehqr\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"gtf\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "b4e1d984bbab555b", + "src": "hda", + "uuid": "6f8b6e2c-3488-4f01-a1df-84612e210d46" + } + }, + "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-24-09-23-06-12-1/errors/e95aae6cbd239ce4.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/e95aae6cbd239ce4.json new file mode 100644 index 000000000..d752eda38 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/e95aae6cbd239ce4.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "e95aae6cbd239ce4", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:23:56.254671", + "update_time": "2024-09-23T07:24:06.737574", + "galaxy_version": "24.1", + "external_id": "gxy-tl525", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/230/registry.xml' '/galaxy/server/database/jobs_directory/000/230/upload_params.json' '285:/galaxy/server/database/objects/2/4/2/dataset_242e1021-b12a-4bba-bbef-bac15bfaa8e3_files:/galaxy/server/database/objects/2/4/2/dataset_242e1021-b12a-4bba-bbef-bac15bfaa8e3.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_6y0wsa7o\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"1000trimmed.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_mkrh0p3o\", \"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": "df13e419be371cb2", + "src": "hda", + "uuid": "242e1021-b12a-4bba-bbef-bac15bfaa8e3" + } + }, + "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-24-09-23-06-12-1/errors/e9cb79a187bc179e.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/e9cb79a187bc179e.json new file mode 100644 index 000000000..0d835f21f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/e9cb79a187bc179e.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "e9cb79a187bc179e", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:33:12.710342", + "update_time": "2024-09-23T07:33:24.631805", + "galaxy_version": "24.1", + "external_id": "gxy-q5k99", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/274/registry.xml' '/galaxy/server/database/jobs_directory/000/274/upload_params.json' '349:/galaxy/server/database/objects/7/e/f/dataset_7ef771f6-df4a-42f4-9951-229cfd2f53eb_files:/galaxy/server/database/objects/7/e/f/dataset_7ef771f6-df4a-42f4-9951-229cfd2f53eb.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_beac5y70\"", + "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"pbmc_1k_v2_L001.R1.10k.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ak832bbd\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "769d715f94162a69", + "src": "hda", + "uuid": "7ef771f6-df4a-42f4-9951-229cfd2f53eb" + } + }, + "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-24-09-23-06-12-1/errors/ef33e62ed7cc0470.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/ef33e62ed7cc0470.json new file mode 100644 index 000000000..9a009037d --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/ef33e62ed7cc0470.json @@ -0,0 +1,53 @@ +{ + "model_class": "Job", + "id": "ef33e62ed7cc0470", + "history_id": "abbc0a781ea0cf97", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T06:57:04.117047", + "update_time": "2024-09-23T06:57:09.697897", + "galaxy_version": "24.1", + "external_id": "gxy-cz2cb", + "handler": null, + "job_runner_name": null, + "command_line": "ln -f -s '/galaxy/server/database/objects/6/6/5/dataset_665f5959-d978-43b5-88f6-d15616b4d500.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'TTAGACATATCTCCGTCG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-trimmed --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_selector": null, + "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", + "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": true, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", + "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", + "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", + "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 145, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"TTAGACATATCTCCGTCG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}" + }, + "inputs": { + "library|input_1": { + "id": "1c94a0697c8cb3cc", + "src": "hda", + "uuid": "665f5959-d978-43b5-88f6-d15616b4d500" + } + }, + "outputs": { + "out1": { + "id": "5772f72a02a89bf1", + "src": "hda", + "uuid": "f5b30055-4f49-4586-ae0a-07ac51200bec" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a TTAGACATATCTCCGTCG --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-trimmed --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (13716.936 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 2 (66.7%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 1 (33.3%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 34 bp (33.3%)\n\n=== Adapter 1 ===\n\nSequence: TTAGACATATCTCCGTCG; Type: regular 3'; Length: 18; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-18 bp: 1\n\nBases preceding removed adapters:\n A: 50.0%\n C: 50.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n10\t1\t0.0\t1\t0 1\n12\t1\t0.0\t1\t0 1\n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a TTAGACATATCTCCGTCG --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-trimmed --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (13716.936 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 2 (66.7%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 1 (33.3%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 34 bp (33.3%)\n\n=== Adapter 1 ===\n\nSequence: TTAGACATATCTCCGTCG; Type: regular 3'; Length: 18; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-18 bp: 1\n\nBases preceding removed adapters:\n A: 50.0%\n C: 50.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n10\t1\t0.0\t1\t0 1\n12\t1\t0.0\t1\t0 1\n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/f0608cd40efb51d8.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/f0608cd40efb51d8.json new file mode 100644 index 000000000..ba3f87f80 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/f0608cd40efb51d8.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "f0608cd40efb51d8", + "history_id": "abbc0a781ea0cf97", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-23T07:39:00.549174", + "update_time": "2024-09-23T07:39:11.659619", + "galaxy_version": "24.1", + "external_id": "gxy-cvg8c", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/320/registry.xml' '/galaxy/server/database/jobs_directory/000/320/upload_params.json' '410:/galaxy/server/database/objects/7/1/f/dataset_71fd2928-50c7-443a-bd86-11de9a5912fa_files:/galaxy/server/database/objects/7/1/f/dataset_71fd2928-50c7-443a-bd86-11de9a5912fa.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_baqkgftn\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_7z7wmcjd\", \"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": "c989d24b5b78dc14", + "src": "hda", + "uuid": "71fd2928-50c7-443a-bd86-11de9a5912fa" + } + }, + "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-24-09-23-06-12-1/errors/fec5d94b97744176.json b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/fec5d94b97744176.json new file mode 100644 index 000000000..8d9c74e54 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/errors/fec5d94b97744176.json @@ -0,0 +1,107 @@ +{ + "model_class": "Job", + "id": "fec5d94b97744176", + "history_id": "abbc0a781ea0cf97", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", + "state": "error", + "exit_code": 1, + "create_time": "2024-09-23T07:18:43.273538", + "update_time": "2024-09-23T07:18:56.488190", + "galaxy_version": "24.1", + "external_id": "gxy-snjfb", + "handler": null, + "job_runner_name": null, + "command_line": "ln -f -s '/galaxy/server/database/objects/6/b/2/dataset_6b23f6b9-3de3-4e6f-94b1-d977648ed349.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/6/9/f/dataset_69ff2f45-a382-4181-a720-19f348b1eebd.dat' 'bwa-mem-fastq_mispaired2_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz' 'bwa-mem-fastq_mispaired2_fq_gz.fq.gz'", + "user_email": "tests@fake.org", + "command_version": "4.9", + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_selector": null, + "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", + "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", + "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", + "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", + "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 254, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 255, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}" + }, + "inputs": { + "library|input_2": { + "id": "e163c494cd39d3a3", + "src": "hda", + "uuid": "69ff2f45-a382-4181-a720-19f348b1eebd" + }, + "library|input_1": { + "id": "c4884b7ca97dac41", + "src": "hda", + "uuid": "6b23f6b9-3de3-4e6f-94b1-d977648ed349" + } + }, + "outputs": { + "out2": { + "id": "c1f040d4177fdc64", + "src": "hda", + "uuid": "6ead2641-954c-4b84-9264-0e3b41e8da7b" + }, + "out1": { + "id": "933f5b704cc607b0", + "src": "hda", + "uuid": "859fc391-6fe9-4d36-abc7-74356823ce10" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq_mispaired2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\n", + "tool_stderr": "Error in sequence file at unknown line: Reads are improperly paired. Read name 'M01368:8:000000000-A3GHV:1:1101:6911:8255/1' in file 1 does not match 'M01368:8:000000000-A3GHV:1:1101:14518:9998/2' in file 2.\n", + "job_stdout": "", + "job_stderr": "", + "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq_mispaired2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\n", + "stderr": "Error in sequence file at unknown line: Reads are improperly paired. Read name 'M01368:8:000000000-A3GHV:1:1101:6911:8255/1' in file 1 does not match 'M01368:8:000000000-A3GHV:1:1101:14518:9998/2' in file 2.\n", + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 1 ()", + "error_level": 3, + "exit_code": 1, + "type": "exit_code" + } + ], + "dependencies": [], + "job_metrics": [ + { + "title": "Job Runtime (Wall Clock)", + "value": "0 seconds", + "plugin": "core", + "name": "runtime_seconds", + "raw_value": "0E-7" + }, + { + "title": "Job End Time", + "value": "2024-09-23 07:18:45", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1727075925.0000000" + }, + { + "title": "Job Start Time", + "value": "2024-09-23 07:18:45", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1727075925.0000000" + }, + { + "title": "Memory Allocated (MB)", + "value": "20401", + "plugin": "core", + "name": "galaxy_memory_mb", + "raw_value": "20401.0000000" + }, + { + "title": "Cores Allocated", + "value": "5", + "plugin": "core", + "name": "galaxy_slots", + "raw_value": "5.0000000" + } + ] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/job-metrics.csv b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/job-metrics.csv new file mode 100644 index 000000000..3faa2842b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/job-metrics.csv @@ -0,0 +1,486 @@ +id,history_id,history_name,state,tool_id,invocation_id,workflow_id,cpuacct.usage,galaxy_memory_mb,galaxy_slots,memory.limit_in_bytes,memory.peak,memory.soft_limit_in_bytes,memtotal,processor_count,runtime_seconds +fca5fc051c4ad73e,abbc0a781ea0cf97,anvil-test-2024-09-23-06-26,ok,vcfdistance/1.0.0_rc3+galaxy0,,,,4080.0000000,1.0000000,,,,,,0E-7 +02340a28cff86a05,abbc0a781ea0cf97,anvil-test-2024-09-23-06-26,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +26ef4e8ea87a2796,abbc0a781ea0cf97,anvil-test-2024-09-23-06-26,ok,vcfcheck/1.0.0_rc3+galaxy0,,,,4080.0000000,1.0000000,,,,,,0E-7 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b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/jobs.txt new file mode 100644 index 000000000..053eee049 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-23-06-12-1/jobs.txt @@ -0,0 +1,485 @@ +fca5fc051c4ad73e ok 2024-09-23T08:15:18.810239 toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0 +02340a28cff86a05 ok 2024-09-23T08:15:04.733343 upload1 +26ef4e8ea87a2796 ok 2024-09-23T08:14:43.581103 toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0 +730230a086e5d7a9 ok 2024-09-23T08:14:23.730213 upload1 +4d48f5e1b172e8fb ok 2024-09-23T08:14:23.639266 upload1 +33349d9168d83366 error 2024-09-23T08:14:01.873314 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4 +c6eba2daf58deee0 ok 2024-09-23T08:13:56.203233 upload1 +df96040a0f260f37 ok 2024-09-23T08:13:37.133719 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4 +c559c752c0eab26f ok 2024-09-23T08:13:23.191429 upload1 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toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4 +a5ba4b94583a4117 ok 2024-09-23T08:09:59.393634 upload1 +92b9f874d38ca583 ok 2024-09-23T08:09:39.249118 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4 +b94bded0304c1f6d ok 2024-09-23T08:09:25.088010 upload1 +c7325399e5e03695 error 2024-09-23T08:09:05.832815 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4 +655d3e84521f61f9 ok 2024-09-23T08:08:59.531651 upload1 +1ce7edabc036d4a6 ok 2024-09-23T08:08:40.347687 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4 +7c7e06db350faed8 ok 2024-09-23T08:08:25.937898 upload1 +60279afdc9b90306 ok 2024-09-23T08:08:06.762044 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4 +b4e1d984bbab555b ok 2024-09-23T08:07:52.988446 upload1 +52c21d65ac1d662f ok 2024-09-23T08:07:33.579480 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4 +6b7c86b97a8ff485 ok 2024-09-23T08:07:14.165584 upload1 +df5f6abe41a2d309 ok 2024-09-23T08:06:52.869154 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4 +5449d4ad7a1879ff ok 2024-09-23T08:06:30.728514 upload1 +003db7640f949660 ok 2024-09-23T08:06:08.588984 toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0 +a6cc817bfc3a7cf1 ok 2024-09-23T08:05:55.161397 upload1 +698ae6f4926183f9 ok 2024-09-23T08:05:34.487112 toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0 +9a832fbfba85c161 ok 2024-09-23T08:05:18.373637 upload1 +170e4d34711da88a ok 2024-09-23T08:04:47.901418 toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2 +5d8fffa9b5064291 ok 2024-09-23T08:04:01.193111 upload1 +0adc3bd0aef531f6 ok 2024-09-23T08:03:37.205812 toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9 +a1ded5dea4d507e6 ok 2024-09-23T08:03:20.622781 upload1 +e901b4616acbf4c6 ok 2024-09-23T08:02:58.420990 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 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toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +c7582cb39596eefa ok 2024-09-23T07:56:54.521464 upload1 +9d03ea77586a8c60 ok 2024-09-23T07:56:54.505036 upload1 +c70c9892e34a53e5 ok 2024-09-23T07:56:33.899829 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +afb967a4f791211a ok 2024-09-23T07:56:19.318773 upload1 +134b51bed63db5da ok 2024-09-23T07:56:19.299752 upload1 +8878c7f506391789 ok 2024-09-23T07:55:58.009467 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +45ecd8724920a9e2 ok 2024-09-23T07:55:44.426357 upload1 +689537b3e9736b1b ok 2024-09-23T07:55:44.312225 upload1 +d0e1e7055efd58d5 ok 2024-09-23T07:55:23.413951 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +c989d24b5b78dc14 ok 2024-09-23T07:55:10.402790 upload1 +116983429b28d5c4 ok 2024-09-23T07:54:50.110537 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +920b4c75f0c9a10a ok 2024-09-23T07:54:35.930783 upload1 +47fa0a5876f8dd81 ok 2024-09-23T07:54:15.150666 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +f4cf0063a73d2c4a ok 2024-09-23T07:54:01.772067 upload1 +327c66d5ff3a6469 ok 2024-09-23T07:53:41.540369 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +cb4beea1623ad968 ok 2024-09-23T07:53:28.610155 upload1 +c36f7f738e22bab8 ok 2024-09-23T07:53:08.310418 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +ddae5651e3915a81 ok 2024-09-23T07:52:54.938391 upload1 +992252542d3a7e8b ok 2024-09-23T07:52:35.096402 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +c4bf7ea85523cc4a ok 2024-09-23T07:52:20.590617 upload1 +386d0735a5dc86d3 ok 2024-09-23T07:52:00.107648 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +3a1879d3bba5a690 ok 2024-09-23T07:51:47.093792 upload1 +bc8e21ef30b30f98 ok 2024-09-23T07:51:26.729364 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +4231b7f2e536216e ok 2024-09-23T07:51:13.191667 upload1 +787e0b7b9546a7d5 ok 2024-09-23T07:50:51.939219 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +c9e9504c62859948 ok 2024-09-23T07:50:38.686288 upload1 +97d23674f5588acb ok 2024-09-23T07:50:18.288952 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +147fcf641b03a326 ok 2024-09-23T07:50:04.028812 upload1 +afb771a7bb55e662 ok 2024-09-23T07:49:43.832112 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +17c139dc68cc7412 ok 2024-09-23T07:49:30.263246 upload1 +a6fe9ef39904e29e ok 2024-09-23T07:49:30.195334 upload1 +c0234df653c5db45 ok 2024-09-23T07:49:09.389120 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +691f644009860ed7 ok 2024-09-23T07:48:55.491718 upload1 +a0ff18d867010488 ok 2024-09-23T07:48:55.449814 upload1 +a2c05ef4a0017263 ok 2024-09-23T07:48:34.842455 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 +4d1ae9689738f953 ok 2024-09-23T07:48:17.416054 upload1 +125fec9e442388a1 ok 2024-09-23T07:47:55.390075 toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1 +7f4a88d8df398ad8 ok 2024-09-23T07:47:39.289454 upload1 +7832d5e7f2f81f0f error 2024-09-23T07:47:17.971108 toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1 +6edda8abcfde41bd ok 2024-09-23T07:47:10.692651 upload1 +e0b8ade3709a9bbc ok 2024-09-23T07:46:49.702328 toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1 +b4e00b74460ff649 ok 2024-09-23T07:46:11.019101 upload1 +e9f97d793d0ce735 ok 2024-09-23T07:46:01.350117 upload1 +dbe0b157c77c0a7f ok 2024-09-23T07:46:01.308846 upload1 +c1cc429ba871f337 ok 2024-09-23T07:46:01.092190 upload1 +99f8cf4b9e420d72 error 2024-09-23T07:45:49.417655 upload1 +6465231d7923c4e0 error 2024-09-23T07:45:49.177066 upload1 +a5d9e0c33d85ffcb ok 2024-09-23T07:45:48.774169 upload1 +f148dc0513eb1566 ok 2024-09-23T07:45:48.330052 upload1 +979348a5a0d3c9f2 ok 2024-09-23T07:45:48.276470 upload1 +a600e72a1eaed9d5 ok 2024-09-23T07:45:48.115495 upload1 +bf62718d3a20ff23 ok 2024-09-23T07:45:31.591648 upload1 +b6b30d78304c60e5 ok 2024-09-23T07:45:30.809537 upload1 +9ff6042cd60b7057 ok 2024-09-23T07:45:30.736518 upload1 +846ffe24b03641b2 ok 2024-09-23T07:45:30.688752 upload1 +50ab40971672b37c ok 2024-09-23T07:45:14.505182 upload1 +bdfcd3fbf37e3201 ok 2024-09-23T07:45:13.506622 upload1 +f6a4e70feba0927c ok 2024-09-23T07:45:13.304287 upload1 +e5c645816530c5e9 ok 2024-09-23T07:45:13.297989 upload1 +5d04a2766377a28d ok 2024-09-23T07:44:57.190875 upload1 +82eefcb619038931 ok 2024-09-23T07:44:55.924737 upload1 +c6361f39b7bb7603 ok 2024-09-23T07:44:55.712641 upload1 +4c47b6ca15d06670 ok 2024-09-23T07:44:55.700574 upload1 +c5dd26505d988ac8 ok 2024-09-23T07:44:32.697701 upload1 +c77a9fa897ef20a0 ok 2024-09-23T07:44:24.208973 upload1 +5e8a6a519aaa54ad ok 2024-09-23T07:44:24.084432 upload1 +7ace0f4c6d1e0d3b ok 2024-09-23T07:44:21.698651 upload1 +c833fa3c005a40ad ok 2024-09-23T07:44:21.643344 upload1 +e3e7a4141b23f3d4 error 2024-09-23T07:44:06.020420 upload1 +c267034d63e0e219 ok 2024-09-23T07:43:46.143068 toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a +769d715f94162a69 ok 2024-09-23T07:43:14.383685 CONVERTER_gz_to_uncompressed +14c4d95fb6b9c7d9 ok 2024-09-23T07:43:00.309717 upload1 +b83a94cb295b94cc ok 2024-09-23T07:42:53.876093 upload1 +c2e5a7224130b76a ok 2024-09-23T07:42:53.311025 upload1 +2140c303132e6f62 ok 2024-09-23T07:42:53.019291 upload1 +5f54b070d4098e3e ok 2024-09-23T07:42:51.383856 upload1 +209a69703347edde ok 2024-09-23T07:42:22.550171 toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a +01b179100d435a0f ok 2024-09-23T07:41:50.633574 CONVERTER_gz_to_uncompressed +6cc7275a431bf448 ok 2024-09-23T07:41:37.203487 upload1 +a1514bea0e3dd162 ok 2024-09-23T07:41:31.905450 upload1 +3ddf6ace9d044ec5 ok 2024-09-23T07:41:30.425261 upload1 +e7d4b1963f7ed440 ok 2024-09-23T07:41:30.385093 upload1 +76878f1130db8d78 ok 2024-09-23T07:41:28.225553 upload1 +eedfaac967aa3c8e ok 2024-09-23T07:41:00.781969 toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a +e7878fa862de1f40 ok 2024-09-23T07:40:29.217628 CONVERTER_gz_to_uncompressed +4fbb27f2f7287fab ok 2024-09-23T07:40:15.652755 upload1 +36cfc8b2bc4633ef ok 2024-09-23T07:40:09.469542 upload1 +0b3a41832b608f87 ok 2024-09-23T07:40:08.717598 upload1 +d319d397f5fd926e ok 2024-09-23T07:40:08.590898 upload1 +beafbf6022086882 ok 2024-09-23T07:40:06.081007 upload1 +1a48a8a5831e526a ok 2024-09-23T07:39:47.699661 upload1 +a405013a715102da ok 2024-09-23T07:39:46.894986 upload1 +c6ad493be844d99a ok 2024-09-23T07:39:39.616483 upload1 +c07355fcd885f3e5 ok 2024-09-23T07:39:39.008820 upload1 +f6cb83298669dabc ok 2024-09-23T07:39:32.130656 upload1 +8b10689ed5d7ab17 error 2024-09-23T07:39:31.210231 upload1 +73008543c518bec9 ok 2024-09-23T07:39:30.876301 upload1 +b21fb1344711fb0c ok 2024-09-23T07:39:28.813294 upload1 +60609b83166bc323 ok 2024-09-23T07:39:26.727093 upload1 +f0608cd40efb51d8 error 2024-09-23T07:39:11.659619 upload1 +22e9ac217513e982 ok 2024-09-23T07:38:57.616927 toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a +186e048eed014707 ok 2024-09-23T07:38:26.330619 CONVERTER_gz_to_uncompressed +9f3b2ba5273306b0 ok 2024-09-23T07:38:11.723438 upload1 +c99502e78aa89fcb ok 2024-09-23T07:38:04.364107 upload1 +a5067bf732c07e8c ok 2024-09-23T07:38:03.725645 upload1 +0d9569971c18e9df ok 2024-09-23T07:38:02.302355 upload1 +7df1c760b33d3870 ok 2024-09-23T07:38:02.287177 upload1 +8707e9b64a16f537 ok 2024-09-23T07:37:40.973712 upload1 +b95b92f3a0573edc ok 2024-09-23T07:37:40.602891 upload1 +2334768aa7fd2c43 ok 2024-09-23T07:37:30.941928 upload1 +c78b432e4d833a49 error 2024-09-23T07:37:30.319444 upload1 +5b2bf096077bd243 error 2024-09-23T07:37:30.027172 upload1 +8c3d34315d165182 error 2024-09-23T07:37:29.702873 upload1 +f6e266c758e7f989 ok 2024-09-23T07:37:29.388436 upload1 +1852ee4c04a25f99 ok 2024-09-23T07:37:29.279234 upload1 +b9fca5aed71d03fe ok 2024-09-23T07:37:29.029963 upload1 +7faec5875443c803 ok 2024-09-23T07:37:11.790171 upload1 +d0b5b8ece218a103 ok 2024-09-23T07:37:10.246723 upload1 +56984c4dd095505f ok 2024-09-23T07:37:10.022340 upload1 +84154a63c3485b7a ok 2024-09-23T07:37:09.529336 upload1 +d42a9ebc0801e970 ok 2024-09-23T07:36:53.497420 upload1 +763ed8a056a24ed9 ok 2024-09-23T07:36:52.979928 upload1 +210169297ad96e00 ok 2024-09-23T07:36:52.927702 upload1 +654fbcfb9e64af94 ok 2024-09-23T07:36:52.609245 upload1 +5148067aa6ded308 ok 2024-09-23T07:36:36.616481 upload1 +87c20641f835b9b7 ok 2024-09-23T07:36:35.662895 upload1 +ae7a4da46530b584 ok 2024-09-23T07:36:35.631445 upload1 +5753ffedd3b75081 ok 2024-09-23T07:36:35.539867 upload1 +6520e1f6478ad976 ok 2024-09-23T07:36:01.871166 toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a +a4947d1fb3e68781 ok 2024-09-23T07:35:46.131287 CONVERTER_gz_to_uncompressed +863f314e05b4c29d ok 2024-09-23T07:35:31.892667 upload1 +cc98b54f0d8e0381 ok 2024-09-23T07:35:31.086845 upload1 +94eb51fbeee9c3e3 ok 2024-09-23T07:35:24.244953 upload1 +0076962bc95703b7 ok 2024-09-23T07:35:24.077955 upload1 +6b28484e5755691b ok 2024-09-23T07:35:22.982968 upload1 +df13e419be371cb2 ok 2024-09-23T07:35:21.176971 upload1 +bdc88e9437af602c ok 2024-09-23T07:34:46.853613 toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a +a8a0896582d6267b ok 2024-09-23T07:34:15.194147 CONVERTER_gz_to_uncompressed +1c229115fa2c6164 ok 2024-09-23T07:34:02.169304 upload1 +e5ba92f5c4e70c76 ok 2024-09-23T07:33:56.429321 upload1 +2f57da5451814566 ok 2024-09-23T07:33:56.336430 upload1 +78d567e71ed12653 ok 2024-09-23T07:33:53.082512 upload1 +9ea3c68bcc40659f ok 2024-09-23T07:33:52.932773 upload1 +2479e8ebff9ce8ef ok 2024-09-23T07:33:40.808836 upload1 +acbce4dc27fa974b ok 2024-09-23T07:33:40.585053 upload1 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toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a +cf4a5f1219ef1fa0 ok 2024-09-23T07:30:09.975464 CONVERTER_gz_to_uncompressed +c1f040d4177fdc64 ok 2024-09-23T07:29:56.098424 upload1 +933f5b704cc607b0 ok 2024-09-23T07:29:49.189028 upload1 +e163c494cd39d3a3 ok 2024-09-23T07:29:49.114365 upload1 +c4884b7ca97dac41 ok 2024-09-23T07:29:47.798586 upload1 +4254a171d8e0a67a ok 2024-09-23T07:29:47.578904 upload1 +38568f59e23ee481 ok 2024-09-23T07:29:16.388259 toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a +89781d424ba22224 ok 2024-09-23T07:28:18.544604 CONVERTER_gz_to_uncompressed +8796d6bd65a7047a ok 2024-09-23T07:28:05.619489 upload1 +f95322f79f3dec14 ok 2024-09-23T07:28:00.730677 upload1 +b202d6941b3eabf3 ok 2024-09-23T07:27:59.933747 upload1 +c749b0c2299daa9f ok 2024-09-23T07:27:59.815697 upload1 +342dfa457583c217 ok 2024-09-23T07:27:55.193167 upload1 +9793c3ab30596a97 error 2024-09-23T07:27:28.784782 upload1 +df4da4e0e70a7cba ok 2024-09-23T07:27:15.829444 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 +7283e8040bdfa16c ok 2024-09-23T07:26:59.036627 upload1 +5c8f33675f7c28a2 ok 2024-09-23T07:26:37.844421 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 +3c89601b05e37c90 ok 2024-09-23T07:26:21.656231 upload1 +983882a617d10737 ok 2024-09-23T07:25:59.544148 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 +8da721664896e4d3 ok 2024-09-23T07:25:43.052759 upload1 +3c9305a78b253272 ok 2024-09-23T07:25:42.781444 upload1 +272286992fb506bb ok 2024-09-23T07:25:21.046475 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 +cf9e963df952ec5d ok 2024-09-23T07:25:05.265971 upload1 +1e1db0cdd2dff83d ok 2024-09-23T07:25:05.188028 upload1 +c7fe15621a9f268d ok 2024-09-23T07:24:43.358794 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 +29c0d8f6b7eac41c ok 2024-09-23T07:24:27.335780 upload1 +5c71d2835951f7f7 ok 2024-09-23T07:24:27.283290 upload1 +c69fa4595c971c31 ok 2024-09-23T07:24:15.591659 upload1 +e95aae6cbd239ce4 error 2024-09-23T07:24:06.737574 upload1 +121d75de73994175 ok 2024-09-23T07:23:54.047337 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 +250d208160e778e4 ok 2024-09-23T07:23:36.780613 upload1 +9e3f9bfea79b9451 ok 2024-09-23T07:23:14.649993 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 +f25e97603549590f ok 2024-09-23T07:22:59.407871 upload1 +810778576ec9a2e4 error 2024-09-23T07:22:39.505538 upload1 +3f96099cf1b666e9 ok 2024-09-23T07:22:26.810113 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 +2f502f8caf6f5267 ok 2024-09-23T07:22:10.881119 upload1 +463ab6aaed89beca ok 2024-09-23T07:21:58.104931 upload1 +49adb5f856bc6730 error 2024-09-23T07:21:50.363149 upload1 +2a78b53ebc84fd37 ok 2024-09-23T07:21:37.405444 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 +69190c74664914bc ok 2024-09-23T07:21:21.508403 upload1 +b77e088473acf86f ok 2024-09-23T07:21:21.463213 upload1 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2024-09-23T07:18:06.563843 upload1 +fdd73cfc0129b814 ok 2024-09-23T07:17:46.490910 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +ccf10959bce65deb ok 2024-09-23T07:17:32.421358 upload1 +2a9a5b9ecd5a6cfc ok 2024-09-23T07:17:11.312734 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +863eb1d47f378dd2 ok 2024-09-23T07:16:58.113569 upload1 +ac76b55aa7119dde ok 2024-09-23T07:16:37.873729 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +78f139cb399786d3 ok 2024-09-23T07:16:22.896065 upload1 +257aab356ba474f6 ok 2024-09-23T07:16:02.719994 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +02d36f70aa6cc8bc ok 2024-09-23T07:15:49.335380 upload1 +44d4d8d711419aa2 ok 2024-09-23T07:15:29.202866 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +440020a6757b7026 ok 2024-09-23T07:15:14.895471 upload1 +e269aaa33e700c1d ok 2024-09-23T07:14:54.618107 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +0e587f8b6a06d925 ok 2024-09-23T07:14:41.699149 upload1 +a169e5c8dd9d4e17 ok 2024-09-23T07:14:21.588495 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +310fb13c87192792 ok 2024-09-23T07:14:07.487993 upload1 +da29229986daa3b5 error 2024-09-23T07:13:48.539885 upload1 +54ec7c8897e748ef ok 2024-09-23T07:13:36.742092 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +b77957ccee766ebc ok 2024-09-23T07:13:23.105600 upload1 +3b88728ede7cf90d ok 2024-09-23T07:13:22.147854 upload1 +4b0a1f8f106498a7 ok 2024-09-23T07:13:10.168396 upload1 +242180e9e118d62b error 2024-09-23T07:13:02.395004 upload1 +f96a7e5905955441 ok 2024-09-23T07:12:50.663226 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +ebf7260e1b00657a ok 2024-09-23T07:12:36.518707 upload1 +aa21f380db82ca21 ok 2024-09-23T07:12:35.601482 upload1 +7ca9ee88b44cb2ef ok 2024-09-23T07:12:24.065271 upload1 +56d12ec3242f54cb error 2024-09-23T07:12:16.197787 upload1 +7cdb4df5cdd75b45 ok 2024-09-23T07:12:04.066387 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +2f301cd90103b119 ok 2024-09-23T07:11:50.834831 upload1 +a4acf38289516d5b ok 2024-09-23T07:11:31.264974 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +c8be1234bd1f6b69 ok 2024-09-23T07:11:16.963139 upload1 +ee4b014024418022 ok 2024-09-23T07:10:56.839990 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +3f861e893e1a6127 ok 2024-09-23T07:10:42.711045 upload1 +583130bd74666373 ok 2024-09-23T07:10:17.838620 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +2b949ef2f85af451 ok 2024-09-23T07:10:03.696271 upload1 +6cf4c296eae030fb ok 2024-09-23T07:09:44.020900 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +0308fa1b7d867675 ok 2024-09-23T07:09:29.073418 upload1 +b809a343ea227e66 ok 2024-09-23T07:09:08.779506 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +6bc787b45fe26419 ok 2024-09-23T07:08:54.592283 upload1 +1a6a5a224659a5e4 ok 2024-09-23T07:08:33.574232 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +0f3aaf74d6fd278f ok 2024-09-23T07:08:19.767738 upload1 +52023b5a9ebebaee ok 2024-09-23T07:08:19.636858 upload1 +ff195f70a972af4b ok 2024-09-23T07:07:59.063905 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +c56f07a7ac133045 ok 2024-09-23T07:07:44.086680 upload1 +a0d6ee61dfd05514 ok 2024-09-23T07:07:43.144006 upload1 +bc29aa6993bd4f81 ok 2024-09-23T07:07:22.516715 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +641bfcc3d43b0b9e ok 2024-09-23T07:07:08.670644 upload1 +4530f5677a812594 ok 2024-09-23T07:07:08.597850 upload1 +58530ce64817ca02 ok 2024-09-23T07:06:46.951542 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +a71f6c5d72119bc6 ok 2024-09-23T07:06:33.314781 upload1 +747972a3e3c020d0 ok 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2024-09-23T06:57:29.858674 upload1 +dcf528637d220b91 ok 2024-09-23T06:57:28.749309 upload1 +ef33e62ed7cc0470 error 2024-09-23T06:57:09.697897 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +fdc095a9f3fc5c3c ok 2024-09-23T06:57:03.721743 upload1 +2eead06849c1ea73 ok 2024-09-23T06:56:44.518438 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +9655f0b6eefaf9e7 ok 2024-09-23T06:56:30.724728 upload1 +2b3d23383ab42ae7 ok 2024-09-23T06:56:30.688580 upload1 +3aae38a2b2c3bea2 ok 2024-09-23T06:56:10.128360 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +fe9fd1ab37024b2e ok 2024-09-23T06:55:56.256345 upload1 +e7f405730f7b4109 ok 2024-09-23T06:55:55.267004 upload1 +dc9e43d48fae261a ok 2024-09-23T06:55:36.568825 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +af09ce9fbd8e19d4 ok 2024-09-23T06:55:22.808457 upload1 +060ca00062cc2f70 ok 2024-09-23T06:55:03.535382 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2024-09-23T06:40:15.568866 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +e0c03c77cb557ef9 ok 2024-09-23T06:40:01.379386 upload1 +be98458bd1f9ff28 ok 2024-09-23T06:39:41.067710 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +0bff8abbb0743dc9 ok 2024-09-23T06:39:26.958867 upload1 +ebcd5746e34a6546 ok 2024-09-23T06:39:06.968767 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +e7183d51460b44d2 ok 2024-09-23T06:38:53.721682 upload1 +56702e342871f40b ok 2024-09-23T06:38:34.449234 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +934fdbce72e9bf00 ok 2024-09-23T06:38:21.390892 upload1 +d56ba89353b1863c ok 2024-09-23T06:38:03.083817 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +b945bb8b7d620815 ok 2024-09-23T06:37:48.952083 upload1 +1d2fe17bc4a2ac2b ok 2024-09-23T06:37:28.658642 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 +5ca1eb1562595f6f ok 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0.15032291412353516, "execution_problem": "Input staging problem: Test input file (anndata_ops.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-4", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 4, "time_seconds": 0.1483771800994873, "execution_problem": "Input staging problem: Test input file (anndata_ops.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-5", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 5, "time_seconds": 0.15134334564208984, "execution_problem": "Input staging problem: Test input file (anndata_ops.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-5", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 5, "time_seconds": 0.14815974235534668, "execution_problem": "Input staging problem: Test input file (anndata_ops.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-6", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 6, "time_seconds": 0.14527559280395508, "execution_problem": "Input staging problem: Test input file (find_cluster.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-6", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 6, "time_seconds": 0.14690065383911133, "execution_problem": "Input staging problem: Test input file (find_cluster.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-7", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 7, "time_seconds": 0.1498267650604248, "execution_problem": "Input staging problem: Test input file (normalise_data.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-7", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 7, "time_seconds": 0.14609551429748535, "execution_problem": "Input staging problem: Test input file (normalise_data.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-8", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 8, "time_seconds": 0.14498567581176758, "execution_problem": "Input staging problem: Test input file (find_cluster.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-8", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 8, "time_seconds": 0.14767146110534668, "execution_problem": "Input staging problem: Test input file (find_cluster.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-9", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 9, "time_seconds": 0.14647793769836426, "execution_problem": "Input staging problem: Test input file (find_cluster.h5) cannot be found.", "status": "error"}}, {"id": "anndata_ops/1.9.3+galaxy0-9", "has_data": true, "data": {"tool_id": "anndata_ops", "tool_version": "1.9.3+galaxy0", "test_index": 9, "time_seconds": 0.14786934852600098, "execution_problem": "Input staging problem: Test input file (find_cluster.h5) cannot be found.", "status": "error"}}, {"id": "bcftools_plugin_counts/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_counts", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 42.51003098487854, "inputs": {"input_file": {"src": "hda", "id": "5c7061f69bb01b62"}}, "job": {"model_class": "Job", "id": "df5f6abe41a2d309", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:06:31.063988", "update_time": "2024-09-23T08:06:52.869154", "galaxy_version": "24.1", "external_id": "gxy-xvdn5", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/c/d/dataset_8cdc8e41-f089-449b-b4e8-a3bb69f9ca7c.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin counts input.vcf.gz | tee counts_file.txt && sed 's/^.* \\([a-zA-Z]*\\):[ ]*\\([0-9]*\\)$/\\1 \\2/' counts_file.txt | python /galaxy/server/database/jobs_directory/000/454/configs/tmpcp8khei3 > '/galaxy/server/database/objects/e/3/f/dataset_e3f166c2-4440-44cb-aca2-d77d47ec9f43.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\"", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "5c7061f69bb01b62", "src": "hda", "uuid": "8cdc8e41-f089-449b-b4e8-a3bb69f9ca7c"}}, "outputs": {"output_file": {"id": "41fcca0e0fb16cee", "src": "hda", "uuid": "e3f166c2-4440-44cb-aca2-d77d47ec9f43"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Number of samples: 3\nNumber of SNPs: 11\nNumber of INDELs: 3\nNumber of MNPs: 0\nNumber of others: 0\nNumber of sites: 15\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Number of samples: 3\nNumber of SNPs: 11\nNumber of INDELs: 3\nNumber of MNPs: 0\nNumber of others: 0\nNumber of sites: 15\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 08:06:39", "plugin": "core", "name": "end_epoch", "raw_value": "1727078799.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:06:38", "plugin": "core", "name": "start_epoch", "raw_value": "1727078798.0000000"}, {"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_view/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_view", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 39.60635828971863, "inputs": {"input_file": {"src": "hda", "id": "af377dc0dcd801e9"}, "sec_subset|samples": "NA00002", "sec_filter|min_ac": "1", "sec_filter|max_ac": "1", "sec_filter|types": "snps", "output_type": "v"}, "job": {"model_class": "Job", "id": "52c21d65ac1d662f", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:07:14.473993", "update_time": "2024-09-23T08:07:33.579480", "galaxy_version": "24.1", "external_id": "gxy-km796", "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/b/c/1/dataset_bc176210-7b59-413f-9f5b-af06b242ee96.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --samples 'NA00002' --min-ac 1 --max-ac 1 --types \"snps\" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/f/4/9/dataset_f49fcd22-87fc-4b23-8f65-f222af1a2667.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": null, \"invert_targets_file\": false}", "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": null, \"max_ac\": \"1\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"1\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": null, \"private\": null, \"select_genotype\": null, \"types\": \"snps\", \"uncalled\": null}", "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"NA00002\", \"samples_file\": null, \"trim_alt_alleles\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "af377dc0dcd801e9", "src": "hda", "uuid": "bc176210-7b59-413f-9f5b-af06b242ee96"}}, "outputs": {"output_file": {"id": "d8e72db659392bf1", "src": "hda", "uuid": "f49fcd22-87fc-4b23-8f65-f222af1a2667"}}, "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": "2024-09-23 08:07:21", "plugin": "core", "name": "end_epoch", "raw_value": "1727078841.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:07:20", "plugin": "core", "name": "start_epoch", "raw_value": "1727078840.0000000"}, {"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_view/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_view", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 33.37308216094971, "inputs": {"input_file": {"src": "hda", "id": "a63845e5608287cc"}, "sec_subset|samples": "NA00002", "sec_filter|min_ac": "1", "sec_filter|max_ac": "1", "sec_filter|types": "snps", "output_type": "v"}, "job": {"model_class": "Job", "id": "60279afdc9b90306", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:07:53.416014", "update_time": "2024-09-23T08:08:06.762044", "galaxy_version": "24.1", "external_id": "gxy-6rt7c", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; ln -s '/galaxy/server/database/objects/e/f/7/dataset_ef72c59e-eb6e-442e-a83b-2286b3482584.dat' input.bcf && ln -s '/galaxy/server/database/objects/_metadata_files/7/5/2/metadata_75268fa3-c4c9-401c-9671-b37ef3197a4b.dat' input.bcf.csi && bcftools view --samples 'NA00002' --min-ac 1 --max-ac 1 --types \"snps\" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.bcf > '/galaxy/server/database/objects/4/b/0/dataset_4b0cb8df-4c1e-453a-94d9-ee46d6b3fc6e.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": null, \"invert_targets_file\": false}", "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": null, \"max_ac\": \"1\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"1\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": null, \"private\": null, \"select_genotype\": null, \"types\": \"snps\", \"uncalled\": null}", "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"NA00002\", \"samples_file\": null, \"trim_alt_alleles\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "a63845e5608287cc", "src": "hda", "uuid": "ef72c59e-eb6e-442e-a83b-2286b3482584"}}, "outputs": {"output_file": {"id": "d45d72aea835f111", "src": "hda", "uuid": "4b0cb8df-4c1e-453a-94d9-ee46d6b3fc6e"}}, "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": "2024-09-23 08:07:55", "plugin": "core", "name": "end_epoch", "raw_value": "1727078875.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:07:55", "plugin": "core", "name": "start_epoch", "raw_value": "1727078875.0000000"}, {"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_view/1.15.1+galaxy4-10", "has_data": true, "data": {"tool_id": "bcftools_view", "tool_version": "1.15.1+galaxy4", "test_index": 10, "time_seconds": 33.99771976470947, "inputs": {"input_file": {"src": "hda", "id": "320ceebfe7357f84"}, "sec_filter|exclude_types": "snps", "sec_output|drop_genotypes": true, "output_type": "v"}, "job": {"model_class": "Job", "id": "b6504558599f2255", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:12:50.962385", "update_time": "2024-09-23T08:13:04.772453", "galaxy_version": "24.1", "external_id": "gxy-4frpz", "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/5/3/8/dataset_538e291a-8f6e-4d8d-956b-40a604a4a0a3.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --exclude-types \"snps\" --drop-genotypes --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/4/6/2/dataset_462579c4-62a1-4b57-b514-674489c39629.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": true, \"header\": null, \"invert_targets_file\": false}", "sec_filter": "{\"exclude_types\": \"snps\", \"known_or_novel\": null, \"max_ac\": \"\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": null, \"private\": null, \"select_genotype\": null, \"types\": null, \"uncalled\": null}", "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"\", \"samples_file\": null, \"trim_alt_alleles\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "320ceebfe7357f84", "src": "hda", "uuid": "538e291a-8f6e-4d8d-956b-40a604a4a0a3"}}, "outputs": {"output_file": {"id": "203f669c8e01ab8b", "src": "hda", "uuid": "462579c4-62a1-4b57-b514-674489c39629"}}, "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": "2024-09-23 08:12:53", "plugin": "core", "name": "end_epoch", "raw_value": "1727079173.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:12:52", "plugin": "core", "name": "start_epoch", "raw_value": "1727079172.0000000"}, {"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_view/1.15.1+galaxy4-11", "has_data": true, "data": {"tool_id": "bcftools_view", "tool_version": "1.15.1+galaxy4", "test_index": 11, "time_seconds": 32.30378985404968, "inputs": {"input_file": {"src": "hda", "id": "bfbb5c73622cbbed"}, "sec_filter|select_genotype": "^het", "sec_filter|phased": "--phased", "output_type": "v"}, "job": {"model_class": "Job", "id": "df96040a0f260f37", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:13:23.714330", "update_time": "2024-09-23T08:13:37.133719", "galaxy_version": "24.1", "external_id": "gxy-dtwqk", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 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"sec_restrict|apply_filters": "PASS", "sec_restrict|regions|regions_0|chrom": "Y", "sec_restrict|regions|regions_0|start": "20", "sec_restrict|regions|regions_src": "regions", "sec_subset|samples": "NA00003", "sec_filter|known_or_novel": "--known", "sec_filter|private": "--exclude-private", "output_type": "v"}, "job": {"model_class": "Job", "id": "c7325399e5e03695", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "error", "exit_code": null, "create_time": "2024-09-23T08:08:59.976222", "update_time": "2024-09-23T08:09:05.832815", "galaxy_version": "24.1", "external_id": "gxy-fn6n2", "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/5/0/dataset_f50aa6f4-2f8b-4202-af6b-13b19268d92f.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --samples 'NA00003' --known --exclude-private --apply-filters 'PASS' --regions 'Y:20-' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/a/9/0/dataset_a90606f7-504f-4563-b5b8-d11e15c5e392.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": null, \"invert_targets_file\": false}", "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": \"--known\", \"max_ac\": \"\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": null, \"private\": \"--exclude-private\", \"select_genotype\": null, \"types\": null, \"uncalled\": null}", "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"NA00003\", \"samples_file\": null, \"trim_alt_alleles\": false}", "sec_restrict": "{\"apply_filters\": \"PASS\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 1, \"regions\": [{\"__index__\": 0, \"chrom\": \"Y\", \"start\": \"20\", \"stop\": null}], \"regions_src\": \"regions\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "4d6697a390ab2b7e", "src": "hda", "uuid": "f50aa6f4-2f8b-4202-af6b-13b19268d92f"}}, "outputs": {"output_file": {"id": "ae59338e30d2df3a", "src": "hda", "uuid": "a90606f7-504f-4563-b5b8-d11e15c5e392"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "bcftools_view/1.15.1+galaxy4-4", "has_data": true, "data": {"tool_id": "bcftools_view", "tool_version": "1.15.1+galaxy4", "test_index": 4, "time_seconds": 33.501434087753296, "inputs": {"input_file": {"src": "hda", "id": "37df6e338c30ae19"}, "sec_subset|samples": "NA00003", "sec_filter|private": "--private", "output_type": "v"}, "job": {"model_class": "Job", "id": "92b9f874d38ca583", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:09:25.363214", "update_time": "2024-09-23T08:09:39.249118", "galaxy_version": "24.1", "external_id": "gxy-s7v9r", "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/9/8/dataset_c98b9f4a-90e2-4af0-b57e-58ffdd6b150e.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --samples 'NA00003' --private --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/8/0/d/dataset_80d535dc-b27e-4b99-a412-ad2b1b97ca5d.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": null, \"invert_targets_file\": false}", "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": null, \"max_ac\": \"\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"\", \"min_af\": \"\", \"min_alleles\": 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"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": "2024-09-23 08:09:27", "plugin": "core", "name": "end_epoch", "raw_value": "1727078967.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:09:26", "plugin": "core", "name": "start_epoch", "raw_value": "1727078966.0000000"}, {"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_view/1.15.1+galaxy4-5", "has_data": true, "data": {"tool_id": "bcftools_view", "tool_version": "1.15.1+galaxy4", "test_index": 5, "time_seconds": 35.65422034263611, "inputs": {"input_file": {"src": "hda", "id": "9507ce3c2555fa61"}, "sec_restrict|include": "QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2", "output_type": "v"}, "job": {"model_class": "Job", "id": "17f577b1735f4812", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:09:59.622727", "update_time": "2024-09-23T08:10:14.904278", "galaxy_version": "24.1", "external_id": "gxy-vxsrv", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/2/4/7/dataset_24736749-bc21-4888-8b40-9cecadb686fb.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --include 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/6/b/2/dataset_6b2dd172-0b4f-41d7-8783-c3fc77c550ae.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": null, \"invert_targets_file\": false}", "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": null, \"max_ac\": \"\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": null, \"private\": null, \"select_genotype\": null, \"types\": null, \"uncalled\": null}", "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"\", \"samples_file\": null, \"trim_alt_alleles\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"exclude\": null, \"include\": \"QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2\", \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "9507ce3c2555fa61", "src": "hda", "uuid": "24736749-bc21-4888-8b40-9cecadb686fb"}}, "outputs": {"output_file": {"id": "d4bebe77007d9f1c", "src": "hda", "uuid": "6b2dd172-0b4f-41d7-8783-c3fc77c550ae"}}, "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": "2024-09-23 08:10:02", "plugin": "core", "name": "end_epoch", "raw_value": "1727079002.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:10:01", "plugin": "core", "name": "start_epoch", "raw_value": "1727079001.0000000"}, {"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_view/1.15.1+galaxy4-6", "has_data": true, "data": {"tool_id": "bcftools_view", "tool_version": "1.15.1+galaxy4", "test_index": 6, "time_seconds": 34.852808237075806, "inputs": {"input_file": {"src": "hda", "id": "0670fe5f3623df63"}, "sec_filter|phased": "--phased", "output_type": "v"}, "job": {"model_class": "Job", "id": "8699c70b6e17d7ab", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:10:35.359012", "update_time": "2024-09-23T08:10:49.990802", "galaxy_version": "24.1", "external_id": "gxy-f9h8k", "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/1/b/dataset_e1b1ba5a-cb78-4a20-aacf-6b831c3234d3.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --phased --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/6/f/f/dataset_6ff5a3fa-9bb7-4ac6-88ab-eddb1c201a33.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": null, \"invert_targets_file\": false}", "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": null, \"max_ac\": \"\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": \"--phased\", \"private\": null, \"select_genotype\": null, \"types\": null, \"uncalled\": null}", "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"\", \"samples_file\": null, \"trim_alt_alleles\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "0670fe5f3623df63", "src": "hda", "uuid": "e1b1ba5a-cb78-4a20-aacf-6b831c3234d3"}}, "outputs": {"output_file": {"id": "d0b1776422e18a1d", "src": "hda", "uuid": "6ff5a3fa-9bb7-4ac6-88ab-eddb1c201a33"}}, "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": "2024-09-23 08:10:38", "plugin": "core", "name": "end_epoch", "raw_value": "1727079038.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:10:37", "plugin": "core", "name": "start_epoch", "raw_value": "1727079037.0000000"}, {"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_view/1.15.1+galaxy4-7", "has_data": true, "data": {"tool_id": "bcftools_view", "tool_version": "1.15.1+galaxy4", "test_index": 7, "time_seconds": 34.178067207336426, "inputs": {"input_file": {"src": "hda", "id": "8444a54719cd7143"}, "sec_filter|phased": "--exclude-phased", "output_type": "v"}, "job": {"model_class": "Job", "id": "5d693c606ad94e2a", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:11:10.289063", "update_time": "2024-09-23T08:11:24.211344", "galaxy_version": "24.1", "external_id": "gxy-8blgz", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/7/3/9/dataset_739d4a40-8709-466f-84d9-00fdaec22490.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --exclude-phased --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/3/e/5/dataset_3e565958-c9cc-4f70-8ae9-0f24181af3f8.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": null, \"invert_targets_file\": false}", "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": null, \"max_ac\": \"\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": \"--exclude-phased\", \"private\": null, \"select_genotype\": null, \"types\": null, \"uncalled\": null}", "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"\", \"samples_file\": null, \"trim_alt_alleles\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "8444a54719cd7143", "src": "hda", "uuid": "739d4a40-8709-466f-84d9-00fdaec22490"}}, "outputs": {"output_file": {"id": "5e8188c6d720f7b8", "src": "hda", "uuid": "3e565958-c9cc-4f70-8ae9-0f24181af3f8"}}, "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": "2024-09-23 08:11:13", "plugin": "core", "name": "end_epoch", "raw_value": "1727079073.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:11:12", "plugin": "core", "name": "start_epoch", "raw_value": "1727079072.0000000"}, {"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_view/1.15.1+galaxy4-8", "has_data": true, "data": {"tool_id": "bcftools_view", "tool_version": "1.15.1+galaxy4", "test_index": 8, "time_seconds": 32.99339699745178, "inputs": {"input_file": {"src": "hda", "id": "e1134bd829bdd869"}, "sec_filter|min_alleles": "2", "sec_filter|max_alleles": "2", "sec_filter|min_af": "0.3", "sec_filter|max_af": "0.7", "sec_output|header": "--header-only", "output_type": "v"}, "job": {"model_class": "Job", "id": "9305c0fde8dc2b3f", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:11:43.760152", "update_time": "2024-09-23T08:11:57.136266", "galaxy_version": "24.1", "external_id": "gxy-7gwhj", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/9/6/7/dataset_967ed43d-ec8b-4826-8b12-78f7b4b34010.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --min-alleles 2 --max-alleles 2 --min-af 0.3 --max-af 0.7 --header-only --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/4/0/1/dataset_401c8b9b-84ae-4456-aeb6-d12033206aed.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": \"--header-only\", \"invert_targets_file\": false}", "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": null, \"max_ac\": \"\", \"max_af\": \"0.7\", \"max_alleles\": \"2\", \"min_ac\": \"\", \"min_af\": \"0.3\", \"min_alleles\": \"2\", \"phased\": null, \"private\": null, \"select_genotype\": null, \"types\": null, \"uncalled\": null}", "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"\", \"samples_file\": null, \"trim_alt_alleles\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "e1134bd829bdd869", "src": "hda", "uuid": "967ed43d-ec8b-4826-8b12-78f7b4b34010"}}, "outputs": {"output_file": {"id": "85e26290b8ba4b63", "src": "hda", "uuid": "401c8b9b-84ae-4456-aeb6-d12033206aed"}}, "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": "2024-09-23 08:11:45", "plugin": "core", "name": "end_epoch", "raw_value": "1727079105.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:11:45", "plugin": "core", "name": "start_epoch", "raw_value": "1727079105.0000000"}, {"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_view/1.15.1+galaxy4-9", "has_data": true, "data": {"tool_id": "bcftools_view", "tool_version": "1.15.1+galaxy4", "test_index": 9, "time_seconds": 33.41800284385681, "inputs": {"input_file": {"src": "hda", "id": "4254c4fda47aa88a"}, "sec_filter|uncalled": "--uncalled", "sec_output|header": "--no-header", "output_type": "v"}, "job": {"model_class": "Job", "id": "3a90f2c63e96ccb8", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:12:16.862159", "update_time": "2024-09-23T08:12:30.878288", "galaxy_version": "24.1", "external_id": "gxy-ftkt4", "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/c/7/dataset_1c703b22-2914-462d-bb39-39f53df60ab5.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools view --uncalled --no-header --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/8/3/a/dataset_83a3f0ed-7c39-4819-b3d3-6f9cef945e3e.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_output": "{\"compression_level\": \"\", \"drop_genotypes\": false, \"header\": \"--no-header\", \"invert_targets_file\": false}", "sec_filter": "{\"exclude_types\": null, \"known_or_novel\": null, \"max_ac\": \"\", \"max_af\": \"\", \"max_alleles\": \"\", \"min_ac\": \"\", \"min_af\": \"\", \"min_alleles\": \"\", \"phased\": null, \"private\": null, \"select_genotype\": null, \"types\": null, \"uncalled\": \"--uncalled\"}", "sec_subset": "{\"force_samples\": false, \"invert_samples\": false, \"invert_samples_file\": false, \"no_update\": false, \"samples\": \"\", \"samples_file\": null, \"trim_alt_alleles\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "4254c4fda47aa88a", "src": "hda", "uuid": "1c703b22-2914-462d-bb39-39f53df60ab5"}}, "outputs": {"output_file": {"id": "90cc6964a87cdd52", "src": "hda", "uuid": "83a3f0ed-7c39-4819-b3d3-6f9cef945e3e"}}, "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": "2024-09-23 08:12:19", "plugin": "core", "name": "end_epoch", "raw_value": "1727079139.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:12:19", "plugin": "core", "name": "start_epoch", "raw_value": "1727079139.0000000"}, {"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": "cutadapt/4.9+galaxy1-0", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 0, "time_seconds": 40.13127517700195, "inputs": {"library|input_1": {"src": "hda", "id": "78731c6a5c429418"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single"}, "job": {"model_class": "Job", "id": "5bb4b82a19d7f1fd", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:29:35.786845", "update_time": "2024-09-23T06:29:55.216644", "galaxy_version": "24.1", "external_id": "gxy-q8d78", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/6/1/c/dataset_61c6c20c-2b3c-46a5-92b0-71b869ee9799.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 5, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "78731c6a5c429418", "src": "hda", "uuid": "61c6c20c-2b3c-46a5-92b0-71b869ee9799"}}, "outputs": {"out1": {"id": "5bb4b82a19d7f1fd", "src": "hda", "uuid": "1908dd07-cede-42c1-afdd-f1bedd2ccaf8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (13620.774 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (13620.774 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:29:42", "plugin": "core", "name": "end_epoch", "raw_value": "1727072982.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:29:41", "plugin": "core", "name": "start_epoch", "raw_value": "1727072981.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-0", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 0, "time_seconds": 32.772321939468384, "inputs": {"library|input_1": {"src": "hda", "id": "6a6bd8bd4377902d"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single"}, "job": {"model_class": "Job", "id": "060ca00062cc2f70", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:54:49.266473", "update_time": "2024-09-23T06:55:03.535382", "galaxy_version": "24.1", "external_id": "gxy-gx2r5", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/f/7/1/dataset_f7142fdc-5e76-42a9-ad5c-18ddc0d6a685.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 133, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "6a6bd8bd4377902d", "src": "hda", "uuid": "f7142fdc-5e76-42a9-ad5c-18ddc0d6a685"}}, "outputs": {"out1": {"id": "c214a78da6b0c5a0", "src": "hda", "uuid": "3d8b34f4-65c9-426f-9ecd-d5b2f1be34e3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (14003.515 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (14003.515 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:54:51", "plugin": "core", "name": "end_epoch", "raw_value": "1727074491.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:54:51", "plugin": "core", "name": "start_epoch", "raw_value": "1727074491.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-1", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 1, "time_seconds": 35.52971577644348, "inputs": {"library|input_1": {"src": "hda", "id": "4851fe9e1c1e44c5"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single"}, "job": {"model_class": "Job", "id": "1d9a06d3201fe113", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:30:16.207724", "update_time": "2024-09-23T06:30:30.784579", "galaxy_version": "24.1", "external_id": "gxy-9nj7s", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/7/c/1/dataset_7c1aba5d-dd45-447d-8de9-bdcd6e3bc8dc.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 7, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "output_selector": null, "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"library|input_1": {"id": "4851fe9e1c1e44c5", "src": "hda", "uuid": "7c1aba5d-dd45-447d-8de9-bdcd6e3bc8dc"}}, "outputs": {"out1": {"id": "1d9a06d3201fe113", "src": "hda", "uuid": "897f02f0-06b7-45fb-831d-2634e95919f6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.103 s (1040.777 \u00b5s/read; 0.06 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 2 (2.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nTotal written (filtered): 24,843 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.103 s (1040.777 \u00b5s/read; 0.06 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 2 (2.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nTotal written (filtered): 24,843 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:30:20", "plugin": "core", "name": "end_epoch", "raw_value": "1727073020.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:30:19", "plugin": "core", "name": "start_epoch", "raw_value": "1727073019.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-1", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 1, "time_seconds": 32.769280433654785, "inputs": {"library|input_1": {"src": "hda", "id": "adaafe605d9e3868"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single"}, "job": {"model_class": "Job", "id": "dc9e43d48fae261a", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:55:23.165108", "update_time": "2024-09-23T06:55:36.568825", "galaxy_version": "24.1", "external_id": "gxy-sbjmv", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/f/9/dataset_5f9d375f-01cd-4e60-bf45-a0e63494b8a4.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 135, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "adaafe605d9e3868", "src": "hda", "uuid": "5f9d375f-01cd-4e60-bf45-a0e63494b8a4"}}, "outputs": {"out1": {"id": "e0074b11b028094a", "src": "hda", "uuid": "86a39f1c-f6aa-4818-bc06-4cac742606e4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.097 s (975.496 \u00b5s/read; 0.06 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 2 (2.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nTotal written (filtered): 24,843 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.097 s (975.496 \u00b5s/read; 0.06 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 2 (2.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nTotal written (filtered): 24,843 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:55:25", "plugin": "core", "name": "end_epoch", "raw_value": "1727074525.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:55:25", "plugin": "core", "name": "start_epoch", "raw_value": "1727074525.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-10", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 10, "time_seconds": 33.36687660217285, "inputs": {"library|input_1": {"src": "hda", "id": "66823dcaa9fca3e3"}, "library|r1|front_adapters_0|adapter_source|adapter_name": "A1", "library|r1|front_adapters_0|adapter_source|adapter": "^GTCGGTAA", "library|r1|front_adapters_0|adapter_source|adapter_source_list": "user", "library|r1|front_adapters_1|adapter_source|adapter_name": "A2", "library|r1|front_adapters_1|adapter_source|adapter": "^AGGTCACT", "library|r1|front_adapters_1|adapter_source|adapter_source_list": "user", "library|type": "single", "output_selector": "multiple_output"}, "job": {"model_class": "Job", "id": "94946436656c3f78", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:34:26.870613", "update_time": "2024-09-23T06:34:39.997426", "galaxy_version": "24.1", "external_id": "gxy-jt7m6", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/c/4/5/dataset_c4518f60-85c2-40fb-94c7-f1f205f742fa.dat' 'cutadapt_in_split_fastq.fq' && mkdir split && cutadapt -j=${GALAXY_SLOTS:-4} -g 'A1'='^GTCGGTAA' -g 'A2'='^AGGTCACT' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'split/{name}.fastq' 'cutadapt_in_split_fastq.fq'", "user_email": "tests@fake.org", "command_version": null, "params": {"library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 32, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"^GTCGGTAA\", \"adapter_name\": \"A1\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}, {\"__index__\": 1, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"^AGGTCACT\", \"adapter_name\": \"A2\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}]}, \"type\": \"single\"}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "output_selector": "\"multiple_output\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"library|input_1": {"id": "66823dcaa9fca3e3", "src": "hda", "uuid": "c4518f60-85c2-40fb-94c7-f1f205f742fa"}}, "outputs": {"__new_primary_file_split_output|A1__": {"id": "739151b03b00fd6d", "src": "hda", "uuid": "4995404a-302b-431e-9e25-f37cb934a591"}, "__new_primary_file_split_output|A2__": {"id": "dcf1626452681bd1", "src": "hda", "uuid": "a5055464-2d7e-4860-bddc-b8d7c8ba9604"}, "__new_primary_file_split_output|unknown__": {"id": "f9119d83db063622", "src": "hda", "uuid": "cfe78b0c-c6b3-447f-9cb0-5cb1e8ed2fd5"}}, "copied_from_job_id": null, "output_collections": {"split_output": {"src": "hdca", "id": "92eb80a7dc7367fd"}}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -g A1=^GTCGGTAA -g A2=^AGGTCACT --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o split/{name}.fastq cutadapt_in_split_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.063 s (5719.857 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 11\nReads with adapters: 10 (90.9%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads discarded as untrimmed: 0 (0.0%)\nReads written (passing filters): 11 (100.0%)\n\nTotal basepairs processed: 1,210 bp\nTotal written (filtered): 1,130 bp (93.4%)\n\n=== Adapter A1 ===\n\nSequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n\n\n=== Adapter A2 ===\n\nSequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -g A1=^GTCGGTAA -g A2=^AGGTCACT --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o split/{name}.fastq cutadapt_in_split_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.063 s (5719.857 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 11\nReads with adapters: 10 (90.9%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads discarded as untrimmed: 0 (0.0%)\nReads written (passing filters): 11 (100.0%)\n\nTotal basepairs processed: 1,210 bp\nTotal written (filtered): 1,130 bp (93.4%)\n\n=== Adapter A1 ===\n\nSequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n\n\n=== Adapter A2 ===\n\nSequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:34:28", "plugin": "core", "name": "start_epoch", "raw_value": "1727073268.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:34:29", "plugin": "core", "name": "end_epoch", "raw_value": "1727073269.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-10", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 10, "time_seconds": 32.51221537590027, "inputs": {"library|input_1": {"src": "hda", "id": "bc29aa6993bd4f81"}, "library|r1|front_adapters_0|adapter_source|adapter_name": "A1", "library|r1|front_adapters_0|adapter_source|adapter": "^GTCGGTAA", "library|r1|front_adapters_0|adapter_source|adapter_source_list": "user", "library|r1|front_adapters_1|adapter_source|adapter_name": "A2", "library|r1|front_adapters_1|adapter_source|adapter": "^AGGTCACT", "library|r1|front_adapters_1|adapter_source|adapter_source_list": "user", "library|type": "single", "output_selector": "multiple_output"}, "job": {"model_class": "Job", "id": "1ab195e8b38743af", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:59:43.042726", "update_time": "2024-09-23T06:59:55.535032", "galaxy_version": "24.1", "external_id": "gxy-8bzbv", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/0/e/dataset_50e3cbaa-94d6-4b06-be13-0c789da13f65.dat' 'cutadapt_in_split_fastq.fq' && mkdir split && cutadapt -j=${GALAXY_SLOTS:-4} -g 'A1'='^GTCGGTAA' -g 'A2'='^AGGTCACT' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'split/{name}.fastq' 'cutadapt_in_split_fastq.fq'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": "\"multiple_output\"", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 161, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"^GTCGGTAA\", \"adapter_name\": \"A1\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}, {\"__index__\": 1, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"^AGGTCACT\", \"adapter_name\": \"A2\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}]}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "bc29aa6993bd4f81", "src": "hda", "uuid": "50e3cbaa-94d6-4b06-be13-0c789da13f65"}}, "outputs": {"__new_primary_file_split_output|A1__": {"id": "a0d6ee61dfd05514", "src": "hda", "uuid": "dd86d93b-519b-45ab-804a-c9f1b32f186b"}, "__new_primary_file_split_output|A2__": {"id": "c56f07a7ac133045", "src": "hda", "uuid": "d81f06de-4b39-4da4-b46b-947fd67cd826"}, "__new_primary_file_split_output|unknown__": {"id": "ff195f70a972af4b", "src": "hda", "uuid": "dfbde345-e32d-4494-8496-268ee55cfbb7"}}, "copied_from_job_id": null, "output_collections": {"split_output": {"src": "hdca", "id": "c5cf6b2dd288fef9"}}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -g A1=^GTCGGTAA -g A2=^AGGTCACT --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o split/{name}.fastq cutadapt_in_split_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.064 s (5789.085 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 11\nReads with adapters: 10 (90.9%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads discarded as untrimmed: 0 (0.0%)\nReads written (passing filters): 11 (100.0%)\n\nTotal basepairs processed: 1,210 bp\nTotal written (filtered): 1,130 bp (93.4%)\n\n=== Adapter A1 ===\n\nSequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n\n\n=== Adapter A2 ===\n\nSequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -g A1=^GTCGGTAA -g A2=^AGGTCACT --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o split/{name}.fastq cutadapt_in_split_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.064 s (5789.085 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 11\nReads with adapters: 10 (90.9%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads discarded as untrimmed: 0 (0.0%)\nReads written (passing filters): 11 (100.0%)\n\nTotal basepairs processed: 1,210 bp\nTotal written (filtered): 1,130 bp (93.4%)\n\n=== Adapter A1 ===\n\nSequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n\n\n=== Adapter A2 ===\n\nSequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:59:45", "plugin": "core", "name": "end_epoch", "raw_value": "1727074785.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:59:44", "plugin": "core", "name": "start_epoch", "raw_value": "1727074784.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-11", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 11, "time_seconds": 35.164316177368164, "inputs": {"library|input_1": {"src": "hda", "id": "6e9c4ec957da5105"}, "library|r1|front_adapters_0|adapter_source|adapter_file": {"src": "hda", "id": "5ca1eb1562595f6f"}, "library|r1|front_adapters_0|adapter_source|adapter_source_list": "file", "library|type": "single", "output_selector": "multiple_output"}, "job": {"model_class": "Job", "id": "02ee2ca586d13cce", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:35:02.031896", "update_time": "2024-09-23T06:35:15.370833", "galaxy_version": "24.1", "external_id": "gxy-kdbjx", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/3/2/3/dataset_3233a0d0-919e-4f63-b6c5-478035822648.dat' 'cutadapt_in_split_fastq_gz.fq.gz' && mkdir split && cutadapt -j=${GALAXY_SLOTS:-4} -g file:'/galaxy/server/database/objects/4/7/3/dataset_47322470-bed3-456a-a991-9cd0d5dff262.dat' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'split/{name}.fastq.gz' 'cutadapt_in_split_fastq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": null, "params": {"library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 36, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 2, \"adapter_file\": {\"values\": [{\"id\": 37, \"src\": \"hda\"}]}, \"adapter_source_list\": \"file\"}, \"single_noindels\": false}]}, \"type\": \"single\"}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "output_selector": "\"multiple_output\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"library|r1|front_adapters_0|adapter_source|adapter_file": {"id": "5ca1eb1562595f6f", "src": "hda", "uuid": "47322470-bed3-456a-a991-9cd0d5dff262"}, "library|input_1": {"id": "6e9c4ec957da5105", "src": "hda", "uuid": "3233a0d0-919e-4f63-b6c5-478035822648"}}, "outputs": {"__new_primary_file_split_output|A1__": {"id": "1d2fe17bc4a2ac2b", "src": "hda", "uuid": "3e7f1e1a-0576-4732-a786-32731a9f67c7"}, "__new_primary_file_split_output|A2__": {"id": "b945bb8b7d620815", "src": "hda", "uuid": "f686c34f-c5fc-47b2-8e86-457f99d3425f"}, "__new_primary_file_split_output|unknown__": {"id": "d56ba89353b1863c", "src": "hda", "uuid": "00345373-2a8d-42a4-b5b8-fd5fbe8cca59"}}, "copied_from_job_id": null, "output_collections": {"split_output": {"src": "hdca", "id": "376b402441ccf867"}}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -g file:/galaxy/server/database/objects/4/7/3/dataset_47322470-bed3-456a-a991-9cd0d5dff262.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o split/{name}.fastq.gz cutadapt_in_split_fastq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.230 s (20892.230 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 11\nReads with adapters: 10 (90.9%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads discarded as untrimmed: 0 (0.0%)\nReads written (passing filters): 11 (100.0%)\n\nTotal basepairs processed: 1,210 bp\nTotal written (filtered): 1,130 bp (93.4%)\n\n=== Adapter A2 ===\n\nSequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n\n\n=== Adapter A1 ===\n\nSequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -g file:/galaxy/server/database/objects/4/7/3/dataset_47322470-bed3-456a-a991-9cd0d5dff262.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o split/{name}.fastq.gz cutadapt_in_split_fastq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.230 s (20892.230 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 11\nReads with adapters: 10 (90.9%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads discarded as untrimmed: 0 (0.0%)\nReads written (passing filters): 11 (100.0%)\n\nTotal basepairs processed: 1,210 bp\nTotal written (filtered): 1,130 bp (93.4%)\n\n=== Adapter A2 ===\n\nSequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n\n\n=== Adapter A1 ===\n\nSequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times\n\nNo. of allowed errors: 0\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t5\t0.0\t0\t5\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:35:03", "plugin": "core", "name": "start_epoch", "raw_value": "1727073303.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:35:04", "plugin": "core", "name": "end_epoch", "raw_value": "1727073304.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-11", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 11, "time_seconds": 13.195790529251099, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "cutadapt/4.9+galaxy1-12", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 12, "time_seconds": 33.56006741523743, "inputs": {"library|input_1": {"src": "hda", "id": "934fdbce72e9bf00"}, "library|r1|adapters_0|adapter_source|adapter": "AAAT", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "output_selector": "untrimmed_file"}, "job": {"model_class": "Job", "id": "df0cf971a23d18a1", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:35:34.826467", "update_time": "2024-09-23T06:35:48.858690", "galaxy_version": "24.1", "external_id": "gxy-rqs6h", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/0/4/e/dataset_04e25d3a-e3ee-47c7-b32a-84d7f6348a6b.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AAAT' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output='untrimmed_output.fq' -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": "\"untrimmed_file\"", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 41, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AAAT\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "934fdbce72e9bf00", "src": "hda", "uuid": "04e25d3a-e3ee-47c7-b32a-84d7f6348a6b"}}, "outputs": {"out1": {"id": "56702e342871f40b", "src": "hda", "uuid": "e9bf59dd-5df6-4e91-8d81-c818c4d3e332"}, "untrimmed_output": {"id": "e7183d51460b44d2", "src": "hda", "uuid": "9e25fc01-e04e-4ed8-92ed-e8c8ca9eef95"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AAAT --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output=untrimmed_output.fq -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.049 s (16285.737 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 1 (33.3%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 30 bp (29.4%)\n\n=== Adapter 1 ===\n\nSequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-4 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n4\t1\t0.0\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AAAT --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output=untrimmed_output.fq -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.049 s (16285.737 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 1 (33.3%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 30 bp (29.4%)\n\n=== Adapter 1 ===\n\nSequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-4 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n4\t1\t0.0\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:35:36", "plugin": "core", "name": "start_epoch", "raw_value": "1727073336.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:35:37", "plugin": "core", "name": "end_epoch", "raw_value": "1727073337.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-12", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 12, "time_seconds": 35.00213623046875, "inputs": {"library|input_1": {"src": "hda", "id": "1a6a5a224659a5e4"}, "library|r1|adapters_0|adapter_source|adapter": "AAAT", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "output_selector": "untrimmed_file"}, "job": {"model_class": "Job", "id": "c214a78da6b0c5a0", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:00:28.623420", "update_time": "2024-09-23T07:00:43.471757", "galaxy_version": "24.1", "external_id": "gxy-8zf2g", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/4/d/e/dataset_4deac394-3aa9-4efa-bc86-cbb44c46f9fb.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AAAT' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output='untrimmed_output.fq' -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": "\"untrimmed_file\"", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 167, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AAAT\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "1a6a5a224659a5e4", "src": "hda", "uuid": "4deac394-3aa9-4efa-bc86-cbb44c46f9fb"}}, "outputs": {"out1": {"id": "6bc787b45fe26419", "src": "hda", "uuid": "109e6b28-3f25-437a-9a0d-8ecf611b6f01"}, "untrimmed_output": {"id": "b809a343ea227e66", "src": "hda", "uuid": "f1529760-b347-42a6-96ff-11ecd7ef4240"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AAAT --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output=untrimmed_output.fq -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.050 s (16743.501 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 1 (33.3%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 30 bp (29.4%)\n\n=== Adapter 1 ===\n\nSequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-4 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n4\t1\t0.0\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AAAT --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output=untrimmed_output.fq -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.050 s (16743.501 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 1 (33.3%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 30 bp (29.4%)\n\n=== Adapter 1 ===\n\nSequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-4 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n4\t1\t0.0\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:00:31", "plugin": "core", "name": "end_epoch", "raw_value": "1727074831.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:00:31", "plugin": "core", "name": "start_epoch", "raw_value": "1727074831.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-13", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 13, "time_seconds": 33.27674961090088, "inputs": {"library|input_1": {"src": "hda", "id": "ebcd5746e34a6546"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "output_selector": "untrimmed_file"}, "job": {"model_class": "Job", "id": "739151b03b00fd6d", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:36:09.082439", "update_time": "2024-09-23T06:36:22.229551", "galaxy_version": "24.1", "external_id": "gxy-bbvt4", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/b/6/8/dataset_b6875ddb-a57b-424e-aae0-6aeaa5c21f6c.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output='untrimmed_output.fq.gz' -o 'out1.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": "\"untrimmed_file\"", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 44, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "ebcd5746e34a6546", "src": "hda", "uuid": "b6875ddb-a57b-424e-aae0-6aeaa5c21f6c"}}, "outputs": {"out1": {"id": "0bff8abbb0743dc9", "src": "hda", "uuid": "c4ba21b8-0720-41f4-8963-99720328495b"}, "untrimmed_output": {"id": "be98458bd1f9ff28", "src": "hda", "uuid": "a60f4479-058e-43e7-ad03-6af8dd0c7afa"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output=untrimmed_output.fq.gz -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.160 s (1613.256 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 2 (2.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (2.0%)\n\nTotal basepairs processed: 24,849 bp\nTotal written (filtered): 496 bp (2.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output=untrimmed_output.fq.gz -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.160 s (1613.256 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 2 (2.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (2.0%)\n\nTotal basepairs processed: 24,849 bp\nTotal written (filtered): 496 bp (2.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:36:10", "plugin": "core", "name": "start_epoch", "raw_value": "1727073370.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:36:11", "plugin": "core", "name": "end_epoch", "raw_value": "1727073371.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-13", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 13, "time_seconds": 24.963846445083618, "inputs": {"library|input_1": {"src": "hda", "id": "0308fa1b7d867675"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "output_selector": "untrimmed_file"}, "job": {"model_class": "Job", "id": "e0074b11b028094a", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-09-23T07:01:03.523812", "update_time": "2024-09-23T07:01:09.297845", "galaxy_version": "24.1", "external_id": "gxy-bvvzs", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/5/f/dataset_d5fec4af-476b-41f1-9fcb-e9ac5aa7e8f5.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output='untrimmed_output.fq.gz' -o 'out1.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": "\"untrimmed_file\"", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 170, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "0308fa1b7d867675", "src": "hda", "uuid": "d5fec4af-476b-41f1-9fcb-e9ac5aa7e8f5"}}, "outputs": {"out1": {"id": "6cf4c296eae030fb", "src": "hda", "uuid": "85a2ecec-c245-4fa1-8f39-fb04c1d3fe04"}, "untrimmed_output": {"id": "2b949ef2f85af451", "src": "hda", "uuid": "542390ae-1de7-49f4-965a-7e19634c592c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output=untrimmed_output.fq.gz -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.159 s (1601.046 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 2 (2.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (2.0%)\n\nTotal basepairs processed: 24,849 bp\nTotal written (filtered): 496 bp (2.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --untrimmed-output=untrimmed_output.fq.gz -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.159 s (1601.046 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 2 (2.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (2.0%)\n\nTotal basepairs processed: 24,849 bp\nTotal written (filtered): 496 bp (2.0%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "cutadapt/4.9+galaxy1-14", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 14, "time_seconds": 33.04177904129028, "inputs": {"library|input_1": {"src": "hda", "id": "e0c03c77cb557ef9"}, "library|input_2": {"src": "hda", "id": "180019349ae3f144"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "filter_options|discard_untrimmed": true, "filter_options|minimum_length": "1", "filter_options|maximum_length": "1000", "filter_options|max_n": "0", "filter_options|pair_filter": "both"}, "job": {"model_class": "Job", "id": "6e9c4ec957da5105", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:36:43.211570", "update_time": "2024-09-23T06:36:56.367317", "galaxy_version": "24.1", "external_id": "gxy-lg2j4", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/f/e/a/dataset_fea29a4c-3f6f-4e82-9421-039956fe931a.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/1/a/1/dataset_1a15a9af-d677-497c-966e-6d3211da3a18.dat' 'bwa-mem-fastq2_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-untrimmed --minimum-length=1 --maximum-length=1000 --max-n=0.0 --pair-filter=both -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz' 'bwa-mem-fastq2_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": true, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"0.0\", \"maximum_length\": \"1000\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"both\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 47, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 48, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "e0c03c77cb557ef9", "src": "hda", "uuid": "fea29a4c-3f6f-4e82-9421-039956fe931a"}, "library|input_2": {"id": "180019349ae3f144", "src": "hda", "uuid": "1a15a9af-d677-497c-966e-6d3211da3a18"}}, "outputs": {"out1": {"id": "20a150f3b7e60ba6", "src": "hda", "uuid": "5bf3e82e-8193-476d-becd-10a03f87e856"}, "out2": {"id": "a38eba43b89f74f1", "src": "hda", "uuid": "d75fcd8a-de75-4e9b-85de-768b03eaf2c0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-untrimmed --minimum-length=1 --maximum-length=1000 --max-n=0.0 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.156 s (1571.429 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 0 (0.0%)\nPairs with too many N: 0 (0.0%)\nPairs written (passing filters): 2 (2.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 998 bp (2.0%)\n Read 1: 496 bp\n Read 2: 502 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-untrimmed --minimum-length=1 --maximum-length=1000 --max-n=0.0 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.156 s (1571.429 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 0 (0.0%)\nPairs with too many N: 0 (0.0%)\nPairs written (passing filters): 2 (2.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 998 bp (2.0%)\n Read 1: 496 bp\n Read 2: 502 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:36:44", "plugin": "core", "name": "start_epoch", "raw_value": "1727073404.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:36:45", "plugin": "core", "name": "end_epoch", "raw_value": "1727073405.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-14", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 14, "time_seconds": 33.874037981033325, "inputs": {"library|input_1": {"src": "hda", "id": "583130bd74666373"}, "library|input_2": {"src": "hda", "id": "3f861e893e1a6127"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "filter_options|discard_untrimmed": true, "filter_options|minimum_length": "1", "filter_options|maximum_length": "1000", "filter_options|max_n": "0", "filter_options|pair_filter": "both"}, "job": {"model_class": "Job", "id": "2dd824f31621a619", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:01:29.481796", "update_time": "2024-09-23T07:01:43.510765", "galaxy_version": "24.1", "external_id": "gxy-qcs6p", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/4/c/dataset_d4cb079d-6fea-4387-bdfc-06c6974dda74.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/0/5/d/dataset_05d3d10c-fd97-485d-9afa-ca6e61257b61.dat' 'bwa-mem-fastq2_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-untrimmed --minimum-length=1 --maximum-length=1000 --max-n=0.0 --pair-filter=both -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz' 'bwa-mem-fastq2_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": true, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"0.0\", \"maximum_length\": \"1000\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"both\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 173, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 174, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "583130bd74666373", "src": "hda", "uuid": "d4cb079d-6fea-4387-bdfc-06c6974dda74"}, "library|input_2": {"id": "3f861e893e1a6127", "src": "hda", "uuid": "05d3d10c-fd97-485d-9afa-ca6e61257b61"}}, "outputs": {"out1": {"id": "ee4b014024418022", "src": "hda", "uuid": "a0897f4c-7344-4fb3-a00f-92e628cb1833"}, "out2": {"id": "c8be1234bd1f6b69", "src": "hda", "uuid": "3e13e25b-9ef4-4cbd-a88e-b23d42fa4b95"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-untrimmed --minimum-length=1 --maximum-length=1000 --max-n=0.0 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.153 s (1545.470 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 0 (0.0%)\nPairs with too many N: 0 (0.0%)\nPairs written (passing filters): 2 (2.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 998 bp (2.0%)\n Read 1: 496 bp\n Read 2: 502 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-untrimmed --minimum-length=1 --maximum-length=1000 --max-n=0.0 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.153 s (1545.470 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 0 (0.0%)\nPairs with too many N: 0 (0.0%)\nPairs written (passing filters): 2 (2.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 998 bp (2.0%)\n Read 1: 496 bp\n Read 2: 502 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:01:31", "plugin": "core", "name": "end_epoch", "raw_value": "1727074891.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:01:31", "plugin": "core", "name": "start_epoch", "raw_value": "1727074891.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-15", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 15, "time_seconds": 32.636332511901855, "inputs": {"library|input_1": {"src": "hda", "id": "94a0cc3705d9b8f1"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|cut": "5"}, "job": {"model_class": "Job", "id": "1d2fe17bc4a2ac2b", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:37:15.809036", "update_time": "2024-09-23T06:37:28.658642", "galaxy_version": "24.1", "external_id": "gxy-wb7jc", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/f/b/e/dataset_fbef4e02-6d9b-47e3-974a-155f5e9b02b2.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"5\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 51, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "94a0cc3705d9b8f1", "src": "hda", "uuid": "fbef4e02-6d9b-47e3-974a-155f5e9b02b2"}}, "outputs": {"out1": {"id": "c52643b1a8f02daa", "src": "hda", "uuid": "9dffe56c-c219-4fc0-9120-7c2d24a7b27f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.045 s (14999.708 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 87 bp (85.3%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.045 s (14999.708 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 87 bp (85.3%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:37:17", "plugin": "core", "name": "start_epoch", "raw_value": "1727073437.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:37:18", "plugin": "core", "name": "end_epoch", "raw_value": "1727073438.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-15", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 15, "time_seconds": 34.67841625213623, "inputs": {"library|input_1": {"src": "hda", "id": "a4acf38289516d5b"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|cut": "5"}, "job": {"model_class": "Job", "id": "dfb1ed8629dfe572", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:02:03.731354", "update_time": "2024-09-23T07:02:17.985851", "galaxy_version": "24.1", "external_id": "gxy-z8s9k", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/4/2/1/dataset_42142309-38f7-430b-805e-77ebe29fddde.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"5\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 177, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "a4acf38289516d5b", "src": "hda", "uuid": "42142309-38f7-430b-805e-77ebe29fddde"}}, "outputs": {"out1": {"id": "2f301cd90103b119", "src": "hda", "uuid": "4a42329a-6a12-4228-a414-81ec20aa0e80"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14226.596 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 87 bp (85.3%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14226.596 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 87 bp (85.3%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:02:06", "plugin": "core", "name": "end_epoch", "raw_value": "1727074926.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:02:05", "plugin": "core", "name": "start_epoch", "raw_value": "1727074925.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-16", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 16, "time_seconds": 34.56294012069702, "inputs": {"library|input_1": {"src": "hda", "id": "3d9c0ca1de18190f"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|cut": "5", "read_mod_options|rename": "{id} barcode={cut_prefix}"}, "job": {"model_class": "Job", "id": "d56ba89353b1863c", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:37:49.079028", "update_time": "2024-09-23T06:38:03.083817", "galaxy_version": "24.1", "external_id": "gxy-xpbtf", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/a/4/f/dataset_a4fc9a62-59fd-4e98-b5b0-b7840b8b2df0.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 --rename='{id} barcode={cut_prefix}' -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": \"{id} barcode={cut_prefix}\", \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"5\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 53, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "3d9c0ca1de18190f", "src": "hda", "uuid": "a4fc9a62-59fd-4e98-b5b0-b7840b8b2df0"}}, "outputs": {"out1": {"id": "012ff491024a103d", "src": "hda", "uuid": "4f91aa9c-bfdc-4e4b-94db-61a5dc774874"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 --rename={id} barcode={cut_prefix} -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.045 s (15043.656 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 87 bp (85.3%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 --rename={id} barcode={cut_prefix} -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.045 s (15043.656 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 87 bp (85.3%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:37:51", "plugin": "core", "name": "start_epoch", "raw_value": "1727073471.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:37:52", "plugin": "core", "name": "end_epoch", "raw_value": "1727073472.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-16", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 16, "time_seconds": 34.28208374977112, "inputs": {"library|input_1": {"src": "hda", "id": "7cdb4df5cdd75b45"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|cut": "5", "read_mod_options|rename": "{id} barcode={cut_prefix}"}, "job": {"model_class": "Job", "id": "0e49637410094e1b", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:02:38.476124", "update_time": "2024-09-23T07:02:52.269673", "galaxy_version": "24.1", "external_id": "gxy-sdqh5", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/4/e/1/dataset_4e10b0e7-1230-4d1e-9ff6-e41e7ea9172f.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 --rename='{id} barcode={cut_prefix}' -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": \"{id} barcode={cut_prefix}\", \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"5\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 179, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "7cdb4df5cdd75b45", "src": "hda", "uuid": "4e10b0e7-1230-4d1e-9ff6-e41e7ea9172f"}}, "outputs": {"out1": {"id": "56d12ec3242f54cb", "src": "hda", "uuid": "8dbf5b3a-396e-4997-bfe1-8e6d24955a6b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 --rename={id} barcode={cut_prefix} -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (13938.745 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 87 bp (85.3%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --cut=5 --minimum-length=1 --rename={id} barcode={cut_prefix} -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (13938.745 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 87 bp (85.3%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:02:41", "plugin": "core", "name": "end_epoch", "raw_value": "1727074961.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:02:40", "plugin": "core", "name": "start_epoch", "raw_value": "1727074960.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-17", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 17, "time_seconds": 31.134507656097412, "inputs": {"library|input_1": {"src": "hda", "id": "bb132b43dc05c202"}, "library|r1|adapters_0|adapter_source|adapter": "CGTCCGAANTAG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|action": "retain"}, "job": {"model_class": "Job", "id": "56702e342871f40b", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:38:21.689034", "update_time": "2024-09-23T06:38:34.449234", "galaxy_version": "24.1", "external_id": "gxy-bsfg7", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/0/1/5/dataset_015d58e0-d259-4858-aa36-c01991286af1.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'CGTCCGAANTAG' --error-rate=0.1 --times=1 --overlap=3 --action=retain --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"retain\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 55, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CGTCCGAANTAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "bb132b43dc05c202", "src": "hda", "uuid": "015d58e0-d259-4858-aa36-c01991286af1"}}, "outputs": {"out1": {"id": "9e8ecd2d45559ef7", "src": "hda", "uuid": "76677ec1-5455-4ccf-b638-67cafbfbc5cb"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=retain --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14222.701 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 80 bp (78.4%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=retain --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14222.701 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 80 bp (78.4%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:38:22", "plugin": "core", "name": "start_epoch", "raw_value": "1727073502.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:38:23", "plugin": "core", "name": "end_epoch", "raw_value": "1727073503.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-17", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 17, "time_seconds": 33.99572014808655, "inputs": {"library|input_1": {"src": "hda", "id": "7ca9ee88b44cb2ef"}, "library|r1|adapters_0|adapter_source|adapter": "CGTCCGAANTAG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|action": "retain"}, "job": {"model_class": "Job", "id": "1c94a0697c8cb3cc", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:03:12.818556", "update_time": "2024-09-23T07:03:26.427032", "galaxy_version": "24.1", "external_id": "gxy-tzpzb", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/a/e/c/dataset_aeced9ac-71df-4b86-8208-f94f92dd652c.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'CGTCCGAANTAG' --error-rate=0.1 --times=1 --overlap=3 --action=retain --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"retain\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 181, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CGTCCGAANTAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "7ca9ee88b44cb2ef", "src": "hda", "uuid": "aeced9ac-71df-4b86-8208-f94f92dd652c"}}, "outputs": {"out1": {"id": "aa21f380db82ca21", "src": "hda", "uuid": "5b179333-6f44-4df7-a1ef-5564d3682fb8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=retain --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (14144.739 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 80 bp (78.4%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=retain --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (14144.739 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 80 bp (78.4%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:03:14", "plugin": "core", "name": "end_epoch", "raw_value": "1727074994.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:03:14", "plugin": "core", "name": "start_epoch", "raw_value": "1727074994.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-18", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 18, "time_seconds": 32.587233781814575, "inputs": {"library|input_1": {"src": "hda", "id": "5841b9f434b3559d"}, "library|r1|adapters_0|adapter_source|adapter": "CGTCCGAANTAG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|action": "mask"}, "job": {"model_class": "Job", "id": "ebcd5746e34a6546", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:38:53.938830", "update_time": "2024-09-23T06:39:06.968767", "galaxy_version": "24.1", "external_id": "gxy-tkdpz", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/a/b/dataset_dabc021a-65ee-477b-8b9f-c3ab471030d9.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'CGTCCGAANTAG' --error-rate=0.1 --times=1 --overlap=3 --action=mask --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"mask\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 57, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CGTCCGAANTAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "5841b9f434b3559d", "src": "hda", "uuid": "dabc021a-65ee-477b-8b9f-c3ab471030d9"}}, "outputs": {"out1": {"id": "7eb3af5995ca0b98", "src": "hda", "uuid": "e710c5db-284a-4613-a6e7-fe73dd3af6ae"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=mask --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.040 s (13287.306 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=mask --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.040 s (13287.306 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:38:55", "plugin": "core", "name": "start_epoch", "raw_value": "1727073535.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:38:56", "plugin": "core", "name": "end_epoch", "raw_value": "1727073536.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-18", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 18, "time_seconds": 32.65217900276184, "inputs": {"library|input_1": {"src": "hda", "id": "ebf7260e1b00657a"}, "library|r1|adapters_0|adapter_source|adapter": "CGTCCGAANTAG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|action": "mask"}, "job": {"model_class": "Job", "id": "ff0dd2107873f620", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:03:45.887990", "update_time": "2024-09-23T07:03:58.943541", "galaxy_version": "24.1", "external_id": "gxy-xr5lc", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/3/9/b/dataset_39bf8034-51e0-41d0-bdad-e8f41d4d49e4.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'CGTCCGAANTAG' --error-rate=0.1 --times=1 --overlap=3 --action=mask --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"mask\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 183, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CGTCCGAANTAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "ebf7260e1b00657a", "src": "hda", "uuid": "39bf8034-51e0-41d0-bdad-e8f41d4d49e4"}}, "outputs": {"out1": {"id": "f96a7e5905955441", "src": "hda", "uuid": "f6fcca59-7039-4add-8cad-efaaf98e52ce"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=mask --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14494.499 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=mask --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14494.499 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:03:47", "plugin": "core", "name": "end_epoch", "raw_value": "1727075027.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:03:47", "plugin": "core", "name": "start_epoch", "raw_value": "1727075027.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-19", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 19, "time_seconds": 33.826451539993286, "inputs": {"library|input_1": {"src": "hda", "id": "36a1f58238c91ace"}, "library|r1|adapters_0|adapter_source|adapter": "CGTCCGAANTAG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|action": "lowercase"}, "job": {"model_class": "Job", "id": "be98458bd1f9ff28", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:39:27.265348", "update_time": "2024-09-23T06:39:41.067710", "galaxy_version": "24.1", "external_id": "gxy-88x4s", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/3/c/f/dataset_3cf89fc9-df5b-4505-8b8b-46ecdac55a9e.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'CGTCCGAANTAG' --error-rate=0.1 --times=1 --overlap=3 --action=lowercase --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"lowercase\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 59, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CGTCCGAANTAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "36a1f58238c91ace", "src": "hda", "uuid": "3cf89fc9-df5b-4505-8b8b-46ecdac55a9e"}}, "outputs": {"out1": {"id": "680ebbbe41fd0738", "src": "hda", "uuid": "240777f0-1e3f-4c3a-82a7-e3d2d7415468"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=lowercase --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.045 s (14935.335 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=lowercase --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.045 s (14935.335 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:39:30", "plugin": "core", "name": "end_epoch", "raw_value": "1727073570.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:39:29", "plugin": "core", "name": "start_epoch", "raw_value": "1727073569.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-19", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 19, "time_seconds": 32.25074505805969, "inputs": {"library|input_1": {"src": "hda", "id": "242180e9e118d62b"}, "library|r1|adapters_0|adapter_source|adapter": "CGTCCGAANTAG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|action": "lowercase"}, "job": {"model_class": "Job", "id": "fe50ce8fea59090d", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:04:18.229778", "update_time": "2024-09-23T07:04:31.349315", "galaxy_version": "24.1", "external_id": "gxy-bwgq7", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/1/f/f/dataset_1ff8cb49-3803-4131-a492-5918da0bd71c.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'CGTCCGAANTAG' --error-rate=0.1 --times=1 --overlap=3 --action=lowercase --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"lowercase\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 185, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CGTCCGAANTAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "242180e9e118d62b", "src": "hda", "uuid": "1ff8cb49-3803-4131-a492-5918da0bd71c"}}, "outputs": {"out1": {"id": "4b0a1f8f106498a7", "src": "hda", "uuid": "1dbd1132-7f22-4527-80e6-8cb1f264c3e3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=lowercase --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (13948.282 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=lowercase --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (13948.282 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:04:20", "plugin": "core", "name": "end_epoch", "raw_value": "1727075060.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:04:19", "plugin": "core", "name": "start_epoch", "raw_value": "1727075059.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-2", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 2, "time_seconds": 37.26064968109131, "inputs": {"library|input_1": {"src": "hda", "id": "d3b28d6e0b2a0e29"}, "library|input_2": {"src": "hda", "id": "4ec27651e3eeecb9"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired"}, "job": {"model_class": "Job", "id": "36226e39681520ef", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:30:52.067190", "update_time": "2024-09-23T06:31:07.399245", "galaxy_version": "24.1", "external_id": "gxy-knsn4", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/1/a/4/dataset_1a4516aa-69ce-4927-8747-d37fd22ce455.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/c/f/9/dataset_cf96e4f1-dd8b-47a6-a13a-b907811bcb30.dat' 'bwa-mem-fastq2_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz' 'bwa-mem-fastq2_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 9, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 10, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "output_selector": null, "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"library|input_2": {"id": "4ec27651e3eeecb9", "src": "hda", "uuid": "cf96e4f1-dd8b-47a6-a13a-b907811bcb30"}, "library|input_1": {"id": "d3b28d6e0b2a0e29", "src": "hda", "uuid": "1a4516aa-69ce-4927-8747-d37fd22ce455"}}, "outputs": {"out2": {"id": "982abeb0f0360d8e", "src": "hda", "uuid": "fe3b95a6-d693-4f28-8f74-d4c8f2f15c51"}, "out1": {"id": "36226e39681520ef", "src": "hda", "uuid": "aa6a2679-85b1-4dd0-8081-9d38988c958c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.173 s (1752.167 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.173 s (1752.167 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:30:55", "plugin": "core", "name": "end_epoch", "raw_value": "1727073055.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:30:54", "plugin": "core", "name": "start_epoch", "raw_value": "1727073054.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-2", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 2, "time_seconds": 34.15709710121155, "inputs": {"library|input_1": {"src": "hda", "id": "e0e8ebd8ec418446"}, "library|input_2": {"src": "hda", "id": "df0c1c11d8ed9191"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired"}, "job": {"model_class": "Job", "id": "3aae38a2b2c3bea2", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:55:56.393599", "update_time": "2024-09-23T06:56:10.128360", "galaxy_version": "24.1", "external_id": "gxy-lccld", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/6/6/dataset_566b4cf6-306f-4e51-95d3-532afaf20377.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/0/e/f/dataset_0efc7628-35dd-4122-98b1-1c8dbc05a5df.dat' 'bwa-mem-fastq2_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz' 'bwa-mem-fastq2_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 137, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 138, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "e0e8ebd8ec418446", "src": "hda", "uuid": "566b4cf6-306f-4e51-95d3-532afaf20377"}, "library|input_2": {"id": "df0c1c11d8ed9191", "src": "hda", "uuid": "0efc7628-35dd-4122-98b1-1c8dbc05a5df"}}, "outputs": {"out1": {"id": "2dd824f31621a619", "src": "hda", "uuid": "3477dd54-7c97-4178-bc66-77f67fe6903b"}, "out2": {"id": "e93cf2160b5ac874", "src": "hda", "uuid": "66ac103e-e50b-4943-9d37-c0cd1b55de2a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.173 s (1745.595 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.173 s (1745.595 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:55:59", "plugin": "core", "name": "end_epoch", "raw_value": "1727074559.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:55:58", "plugin": "core", "name": "start_epoch", "raw_value": "1727074558.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-20", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 20, "time_seconds": 34.67839813232422, "inputs": {"library|input_1": {"src": "hda", "id": "15b2f6de1622d3ab"}, "library|r1|adapters_0|adapter_source|adapter": "CGTCCGAANTAG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|action": "crop"}, "job": {"model_class": "Job", "id": "180019349ae3f144", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:40:01.830465", "update_time": "2024-09-23T06:40:15.568866", "galaxy_version": "24.1", "external_id": "gxy-9zlrf", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/c/d/dataset_dcd7cf2c-3816-491c-85e2-81e51e9a807a.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'CGTCCGAANTAG' --error-rate=0.1 --times=1 --overlap=3 --action=crop --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"crop\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 61, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CGTCCGAANTAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "15b2f6de1622d3ab", "src": "hda", "uuid": "dcd7cf2c-3816-491c-85e2-81e51e9a807a"}}, "outputs": {"out1": {"id": "fc21d19e9f7d6345", "src": "hda", "uuid": "8d388928-75f7-47cb-8d08-c1841e79b44e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=crop --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.045 s (14901.797 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 80 bp (78.4%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=crop --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.045 s (14901.797 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 80 bp (78.4%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:40:03", "plugin": "core", "name": "end_epoch", "raw_value": "1727073603.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:40:03", "plugin": "core", "name": "start_epoch", "raw_value": "1727073603.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-20", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 20, "time_seconds": 33.278374671936035, "inputs": {"library|input_1": {"src": "hda", "id": "3b88728ede7cf90d"}, "library|r1|adapters_0|adapter_source|adapter": "CGTCCGAANTAG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|action": "crop"}, "job": {"model_class": "Job", "id": "e3f5a8c3be19492f", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:04:50.594830", "update_time": "2024-09-23T07:05:04.775457", "galaxy_version": "24.1", "external_id": "gxy-9sswv", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/7/4/8/dataset_74877b1f-280a-4ea2-a1ee-27d02c2ab89a.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'CGTCCGAANTAG' --error-rate=0.1 --times=1 --overlap=3 --action=crop --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"crop\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 187, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CGTCCGAANTAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "3b88728ede7cf90d", "src": "hda", "uuid": "74877b1f-280a-4ea2-a1ee-27d02c2ab89a"}}, "outputs": {"out1": {"id": "b77957ccee766ebc", "src": "hda", "uuid": "45a5feb2-52a8-42fc-8585-3106b9562112"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=crop --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (13818.582 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 80 bp (78.4%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=crop --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (13818.582 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 80 bp (78.4%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:04:53", "plugin": "core", "name": "end_epoch", "raw_value": "1727075093.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:04:52", "plugin": "core", "name": "start_epoch", "raw_value": "1727075092.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-21", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 21, "time_seconds": 33.10483002662659, "inputs": {"library|input_1": {"src": "hda", "id": "20e650b6a023a7b1"}, "library|r1|adapters_0|adapter_source|adapter": "CGTCCGAANTAG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|action": "none"}, "job": {"model_class": "Job", "id": "a38eba43b89f74f1", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:40:35.015640", "update_time": "2024-09-23T06:40:48.898025", "galaxy_version": "24.1", "external_id": "gxy-zmwdt", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/6/8/e/dataset_68ec6eeb-18a1-4645-8bfa-c098128c76bb.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'CGTCCGAANTAG' --error-rate=0.1 --times=1 --overlap=3 --action=none --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"none\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 63, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CGTCCGAANTAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "20e650b6a023a7b1", "src": "hda", "uuid": "68ec6eeb-18a1-4645-8bfa-c098128c76bb"}}, "outputs": {"out1": {"id": "cb9e1138b6558e08", "src": "hda", "uuid": "ca21f9f3-fc34-47ea-b6c3-5ee45a25c0c0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=none --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14320.215 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=none --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14320.215 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:40:37", "plugin": "core", "name": "end_epoch", "raw_value": "1727073637.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:40:37", "plugin": "core", "name": "start_epoch", "raw_value": "1727073637.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-21", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 21, "time_seconds": 33.58710241317749, "inputs": {"library|input_1": {"src": "hda", "id": "54ec7c8897e748ef"}, "library|r1|adapters_0|adapter_source|adapter": "CGTCCGAANTAG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|action": "none"}, "job": {"model_class": "Job", "id": "880f77f39a3c619b", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:05:25.238106", "update_time": "2024-09-23T07:05:38.384453", "galaxy_version": "24.1", "external_id": "gxy-rkdsp", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/b/c/3/dataset_bc3dc45a-cf0d-4802-9c92-5d2b23e9084b.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'CGTCCGAANTAG' --error-rate=0.1 --times=1 --overlap=3 --action=none --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"none\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 189, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CGTCCGAANTAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "54ec7c8897e748ef", "src": "hda", "uuid": "bc3dc45a-cf0d-4802-9c92-5d2b23e9084b"}}, "outputs": {"out1": {"id": "da29229986daa3b5", "src": "hda", "uuid": "90599ee2-24e3-4dde-a4ba-653f83b64b82"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=none --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.044 s (14580.886 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a CGTCCGAANTAG --error-rate=0.1 --times=1 --overlap=3 --action=none --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.044 s (14580.886 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-11 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:05:27", "plugin": "core", "name": "end_epoch", "raw_value": "1727075127.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:05:26", "plugin": "core", "name": "start_epoch", "raw_value": "1727075126.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-22", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 22, "time_seconds": 32.23222827911377, "inputs": {"library|input_1": {"src": "hda", "id": "db928d5e388f7f4d"}, "library|r1|adapters_0|adapter_source|adapter": "TAAACAGATTAGT", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|revcomp": true}, "job": {"model_class": "Job", "id": "c52643b1a8f02daa", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:41:08.458106", "update_time": "2024-09-23T06:41:21.093303", "galaxy_version": "24.1", "external_id": "gxy-ckv5f", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/5/3/dataset_d53cda07-e421-41b1-b8cf-cee9011f5955.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'TAAACAGATTAGT' --error-rate=0.1 --times=1 --overlap=3 --action=trim --rc --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": true, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 65, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"TAAACAGATTAGT\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "db928d5e388f7f4d", "src": "hda", "uuid": "d53cda07-e421-41b1-b8cf-cee9011f5955"}}, "outputs": {"out1": {"id": "bc536437d45eb8d3", "src": "hda", "uuid": "36c614de-8b72-437f-b3e5-475971d87656"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a TAAACAGATTAGT --error-rate=0.1 --times=1 --overlap=3 --action=trim --rc --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.040 s (13425.191 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReverse-complemented: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 97 bp (95.1%)\n\n=== Adapter 1 ===\n\nSequence: TAAACAGATTAGT; Type: regular 3'; Length: 13; Trimmed: 1 times; Reverse-complemented: 0 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n5\t1\t0.0\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a TAAACAGATTAGT --error-rate=0.1 --times=1 --overlap=3 --action=trim --rc --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.040 s (13425.191 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReverse-complemented: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 97 bp (95.1%)\n\n=== Adapter 1 ===\n\nSequence: TAAACAGATTAGT; Type: regular 3'; Length: 13; Trimmed: 1 times; Reverse-complemented: 0 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n5\t1\t0.0\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:41:10", "plugin": "core", "name": "end_epoch", "raw_value": "1727073670.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:41:10", "plugin": "core", "name": "start_epoch", "raw_value": "1727073670.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-22", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 22, "time_seconds": 34.10596537590027, "inputs": {"library|input_1": {"src": "hda", "id": "310fb13c87192792"}, "library|r1|adapters_0|adapter_source|adapter": "TAAACAGATTAGT", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|revcomp": true}, "job": {"model_class": "Job", "id": "b46b3e897455561b", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:05:58.706175", "update_time": "2024-09-23T07:06:12.481727", "galaxy_version": "24.1", "external_id": "gxy-tdgmt", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/7/c/b/dataset_7cb0625f-1f2f-4139-9a19-7124f4cb669a.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'TAAACAGATTAGT' --error-rate=0.1 --times=1 --overlap=3 --action=trim --rc --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": true, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 191, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"TAAACAGATTAGT\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "310fb13c87192792", "src": "hda", "uuid": "7cb0625f-1f2f-4139-9a19-7124f4cb669a"}}, "outputs": {"out1": {"id": "a169e5c8dd9d4e17", "src": "hda", "uuid": "b5c290d9-90fa-4da7-805f-fb77336f155f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a TAAACAGATTAGT --error-rate=0.1 --times=1 --overlap=3 --action=trim --rc --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14441.729 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReverse-complemented: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 97 bp (95.1%)\n\n=== Adapter 1 ===\n\nSequence: TAAACAGATTAGT; Type: regular 3'; Length: 13; Trimmed: 1 times; Reverse-complemented: 0 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n5\t1\t0.0\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a TAAACAGATTAGT --error-rate=0.1 --times=1 --overlap=3 --action=trim --rc --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14441.729 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReverse-complemented: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 97 bp (95.1%)\n\n=== Adapter 1 ===\n\nSequence: TAAACAGATTAGT; Type: regular 3'; Length: 13; Trimmed: 1 times; Reverse-complemented: 0 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n5\t1\t0.0\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:06:01", "plugin": "core", "name": "end_epoch", "raw_value": "1727075161.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:06:00", "plugin": "core", "name": "start_epoch", "raw_value": "1727075160.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-23", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 23, "time_seconds": 19.083638191223145, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "cutadapt/4.9+galaxy1-23", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 23, "time_seconds": 34.92299675941467, "inputs": {"library|input_1": {"src": "hda", "id": "0e587f8b6a06d925"}, "library|input_2": {"src": "hda", "id": "e269aaa33e700c1d"}, "library|r1|adapters_0|adapter_source|adapter": "ATCTGGTTCC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "CTACAAG", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "filter_options|minimum_length": "30", "filter_options|minimum_length2": "10", "filter_options|pair_filter": "both"}, "job": {"model_class": "Job", "id": "58530ce64817ca02", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:06:33.562648", "update_time": "2024-09-23T07:06:46.951542", "galaxy_version": "24.1", "external_id": "gxy-nhl59", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/c/5/e/dataset_c5e91394-3832-4d6d-b9b1-072dc84ab2ce.dat' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/9/e/a/dataset_9eab99b1-5946-4f47-8c95-de1181524ebf.dat' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'ATCTGGTTCC' -A 'CTACAAG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=30:10 --pair-filter=both -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"30\", \"minimum_length2\": \"10\", \"pair_filter\": \"both\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 193, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 194, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"ATCTGGTTCC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"CTACAAG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "0e587f8b6a06d925", "src": "hda", "uuid": "c5e91394-3832-4d6d-b9b1-072dc84ab2ce"}, "library|input_2": {"id": "e269aaa33e700c1d", "src": "hda", "uuid": "9eab99b1-5946-4f47-8c95-de1181524ebf"}}, "outputs": {"out1": {"id": "440020a6757b7026", "src": "hda", "uuid": "1d61e110-4ab5-42ae-852d-e8d1747d3a6d"}, "out2": {"id": "44d4d8d711419aa2", "src": "hda", "uuid": "90ed4298-fbfb-429e-ad41-22560f5aeed2"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a ATCTGGTTCC -A CTACAAG --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=30:10 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.172 s (1739.475 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 32 (32.3%)\n Read 2 with adapter: 15 (15.2%)\n\n== Read fate breakdown ==\nPairs that were too short: 3 (3.0%)\nPairs written (passing filters): 96 (97.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 38,492 bp (79.7%)\n Read 1: 17,741 bp\n Read 2: 20,751 bp\n\n=== First read: Adapter 1 ===\n\nSequence: ATCTGGTTCC; Type: regular 3'; Length: 10; Trimmed: 32 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 90.6%\n G: 3.1%\n T: 0.0%\n none/other: 6.2%\nWARNING:\n The adapter is preceded by 'C' extremely often.\n The provided adapter sequence could be incomplete at its 5' end.\n Ignore this warning when trimming primers.\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n13\t1\t0.0\t1\t1\n14\t1\t0.0\t1\t1\n201\t1\t0.0\t1\t1\n203\t1\t0.0\t1\t1\n208\t2\t0.0\t1\t2\n209\t1\t0.0\t1\t1\n211\t1\t0.0\t1\t1\n214\t2\t0.0\t1\t2\n217\t2\t0.0\t1\t2\n218\t1\t0.0\t1\t1\n222\t1\t0.0\t1\t1\n226\t1\t0.0\t1\t1\n227\t2\t0.0\t1\t2\n228\t1\t0.0\t1\t1\n229\t1\t0.0\t1\t1\n232\t2\t0.0\t1\t2\n238\t1\t0.0\t1\t1\n242\t7\t0.0\t1\t7\n251\t1\t0.0\t1\t0 1\n\n\n=== Second read: Adapter 2 ===\n\nSequence: CTACAAG; Type: regular 3'; Length: 7; Trimmed: 15 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-7 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 73.3%\n G: 0.0%\n T: 0.0%\n none/other: 26.7%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t1\t0.0\t0\t1\n228\t2\t0.0\t0\t2\n229\t1\t0.0\t0\t1\n238\t3\t0.0\t0\t3\n241\t1\t0.0\t0\t1\n243\t1\t0.0\t0\t1\n246\t1\t0.0\t0\t1\n248\t1\t0.0\t0\t1\n250\t1\t0.0\t0\t1\n251\t3\t0.0\t0\t3\n\n\nWARNING:\n One or more of your adapter sequences may be incomplete.\n Please see the detailed output above.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a ATCTGGTTCC -A CTACAAG --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=30:10 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.172 s (1739.475 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 32 (32.3%)\n Read 2 with adapter: 15 (15.2%)\n\n== Read fate breakdown ==\nPairs that were too short: 3 (3.0%)\nPairs written (passing filters): 96 (97.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 38,492 bp (79.7%)\n Read 1: 17,741 bp\n Read 2: 20,751 bp\n\n=== First read: Adapter 1 ===\n\nSequence: ATCTGGTTCC; Type: regular 3'; Length: 10; Trimmed: 32 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 90.6%\n G: 3.1%\n T: 0.0%\n none/other: 6.2%\nWARNING:\n The adapter is preceded by 'C' extremely often.\n The provided adapter sequence could be incomplete at its 5' end.\n Ignore this warning when trimming primers.\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n13\t1\t0.0\t1\t1\n14\t1\t0.0\t1\t1\n201\t1\t0.0\t1\t1\n203\t1\t0.0\t1\t1\n208\t2\t0.0\t1\t2\n209\t1\t0.0\t1\t1\n211\t1\t0.0\t1\t1\n214\t2\t0.0\t1\t2\n217\t2\t0.0\t1\t2\n218\t1\t0.0\t1\t1\n222\t1\t0.0\t1\t1\n226\t1\t0.0\t1\t1\n227\t2\t0.0\t1\t2\n228\t1\t0.0\t1\t1\n229\t1\t0.0\t1\t1\n232\t2\t0.0\t1\t2\n238\t1\t0.0\t1\t1\n242\t7\t0.0\t1\t7\n251\t1\t0.0\t1\t0 1\n\n\n=== Second read: Adapter 2 ===\n\nSequence: CTACAAG; Type: regular 3'; Length: 7; Trimmed: 15 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-7 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 73.3%\n G: 0.0%\n T: 0.0%\n none/other: 26.7%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n8\t1\t0.0\t0\t1\n228\t2\t0.0\t0\t2\n229\t1\t0.0\t0\t1\n238\t3\t0.0\t0\t3\n241\t1\t0.0\t0\t1\n243\t1\t0.0\t0\t1\n246\t1\t0.0\t0\t1\n248\t1\t0.0\t0\t1\n250\t1\t0.0\t0\t1\n251\t3\t0.0\t0\t3\n\n\nWARNING:\n One or more of your adapter sequences may be incomplete.\n Please see the detailed output above.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:06:36", "plugin": "core", "name": "end_epoch", "raw_value": "1727075196.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:06:35", "plugin": "core", "name": "start_epoch", "raw_value": "1727075195.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-24", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 24, "time_seconds": 34.44318771362305, "inputs": {"library|input_1": {"src": "hda", "id": "fc9418bd75c7a473"}, "library|input_2": {"src": "hda", "id": "5c6c599dc19e91f0"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "filter_options|maximum_length": "50", "filter_options|maximum_length2": "30", "filter_options|pair_filter": "both"}, "job": {"model_class": "Job", "id": "5841b9f434b3559d", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:42:00.983765", "update_time": "2024-09-23T06:42:14.467726", "galaxy_version": "24.1", "external_id": "gxy-swbg2", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/2/9/5/dataset_2951c633-ae0e-4b68-8a76-6e5c6e590ef2.dat' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/f/8/2/dataset_f821a212-e410-4d79-a919-c574392684ac.dat' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --maximum-length=50:30 --pair-filter=both -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"50\", \"maximum_length2\": \"30\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"both\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 69, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 70, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "fc9418bd75c7a473", "src": "hda", "uuid": "2951c633-ae0e-4b68-8a76-6e5c6e590ef2"}, "library|input_2": {"id": "5c6c599dc19e91f0", "src": "hda", "uuid": "f821a212-e410-4d79-a919-c574392684ac"}}, "outputs": {"out1": {"id": "cb1d521ab1fd0bb6", "src": "hda", "uuid": "ad48ded3-cbaf-496c-a531-7cfa0025cd13"}, "out2": {"id": "aac6ba61905fd263", "src": "hda", "uuid": "7c7db2b6-24f6-42b6-a233-bac3b3cdc140"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --maximum-length=50:30 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.169 s (1705.825 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --maximum-length=50:30 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.169 s (1705.825 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:42:03", "plugin": "core", "name": "end_epoch", "raw_value": "1727073723.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:42:03", "plugin": "core", "name": "start_epoch", "raw_value": "1727073723.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-24", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 24, "time_seconds": 35.47979164123535, "inputs": {"library|input_1": {"src": "hda", "id": "02d36f70aa6cc8bc"}, "library|input_2": {"src": "hda", "id": "257aab356ba474f6"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "filter_options|maximum_length": "50", "filter_options|maximum_length2": "30", "filter_options|pair_filter": "both"}, "job": {"model_class": "Job", "id": "bc29aa6993bd4f81", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:07:08.840771", "update_time": "2024-09-23T07:07:22.516715", "galaxy_version": "24.1", "external_id": "gxy-2vh2d", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/0/5/dataset_d0567da8-6256-4e52-b0a2-5c601fc984d4.dat' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/d/8/1/dataset_d816348f-5079-456f-bbe7-dfe7e3f408a4.dat' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --maximum-length=50:30 --pair-filter=both -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"50\", \"maximum_length2\": \"30\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"both\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 197, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 198, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "02d36f70aa6cc8bc", "src": "hda", "uuid": "d0567da8-6256-4e52-b0a2-5c601fc984d4"}, "library|input_2": {"id": "257aab356ba474f6", "src": "hda", "uuid": "d816348f-5079-456f-bbe7-dfe7e3f408a4"}}, "outputs": {"out1": {"id": "78f139cb399786d3", "src": "hda", "uuid": "d85df929-b0cf-49b9-96f3-d5986e2ed3f4"}, "out2": {"id": "ac76b55aa7119dde", "src": "hda", "uuid": "7d7a9bdf-2133-43bf-9e53-ad3db59c5235"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --maximum-length=50:30 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.173 s (1745.472 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --maximum-length=50:30 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.173 s (1745.472 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:07:11", "plugin": "core", "name": "end_epoch", "raw_value": "1727075231.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:07:10", "plugin": "core", "name": "start_epoch", "raw_value": "1727075230.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-25", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 25, "time_seconds": 34.46057915687561, "inputs": {"library|input_1": {"src": "hda", "id": "d9035bff43c21374"}, "library|input_2": {"src": "hda", "id": "8aad297c71d58715"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "filter_options|minimum_length": "10", "filter_options|maximum_length": "50", "filter_options|maximum_length2": "30", "filter_options|pair_filter": "both"}, "job": {"model_class": "Job", "id": "680ebbbe41fd0738", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:42:35.597509", "update_time": "2024-09-23T06:42:49.073848", "galaxy_version": "24.1", "external_id": "gxy-sjgxn", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/4/9/2/dataset_492e553b-539a-44fc-a7e4-1cd87080e5ba.dat' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/0/4/8/dataset_04894949-3b13-467d-854b-82fd585abd59.dat' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10 --maximum-length=50:30 --pair-filter=both -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"50\", \"maximum_length2\": \"30\", \"minimum_length\": \"10\", \"minimum_length2\": \"\", \"pair_filter\": \"both\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 73, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 74, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_2": {"id": "8aad297c71d58715", "src": "hda", "uuid": "04894949-3b13-467d-854b-82fd585abd59"}, "library|input_1": {"id": "d9035bff43c21374", "src": "hda", "uuid": "492e553b-539a-44fc-a7e4-1cd87080e5ba"}}, "outputs": {"out1": {"id": "ad74905b0cba1fb9", "src": "hda", "uuid": "d8cfbbd8-79ef-4a52-bd60-2a5e3af496b2"}, "out2": {"id": "b6547e96db8811ba", "src": "hda", "uuid": "fd2527f8-28b5-4855-8fcf-1ddbe6e7c266"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10 --maximum-length=50:30 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.155 s (1568.686 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10 --maximum-length=50:30 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.155 s (1568.686 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:42:37", "plugin": "core", "name": "end_epoch", "raw_value": "1727073757.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:42:37", "plugin": "core", "name": "start_epoch", "raw_value": "1727073757.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-25", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 25, "time_seconds": 36.41721701622009, "inputs": {"library|input_1": {"src": "hda", "id": "863eb1d47f378dd2"}, "library|input_2": {"src": "hda", "id": "2a9a5b9ecd5a6cfc"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "filter_options|minimum_length": "10", "filter_options|maximum_length": "50", "filter_options|maximum_length2": "30", "filter_options|pair_filter": "both"}, "job": {"model_class": "Job", "id": "ff195f70a972af4b", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:07:44.535096", "update_time": "2024-09-23T07:07:59.063905", "galaxy_version": "24.1", "external_id": "gxy-wxlhw", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/1/f/e/dataset_1fe5d5ca-9e7d-4d1b-9259-c2980e8ac8c4.dat' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/d/a/0/dataset_da029573-6b72-4c94-b63a-8c43830b23b7.dat' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10 --maximum-length=50:30 --pair-filter=both -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"50\", \"maximum_length2\": \"30\", \"minimum_length\": \"10\", \"minimum_length2\": \"\", \"pair_filter\": \"both\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 201, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 202, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "863eb1d47f378dd2", "src": "hda", "uuid": "1fe5d5ca-9e7d-4d1b-9259-c2980e8ac8c4"}, "library|input_2": {"id": "2a9a5b9ecd5a6cfc", "src": "hda", "uuid": "da029573-6b72-4c94-b63a-8c43830b23b7"}}, "outputs": {"out1": {"id": "ccf10959bce65deb", "src": "hda", "uuid": "561dfeb8-ba4e-4c09-88b7-1c37754adff3"}, "out2": {"id": "fdd73cfc0129b814", "src": "hda", "uuid": "92038da9-a827-48d0-9247-91f2db24614f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10 --maximum-length=50:30 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.161 s (1631.171 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10 --maximum-length=50:30 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.161 s (1631.171 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:07:46", "plugin": "core", "name": "end_epoch", "raw_value": "1727075266.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:07:46", "plugin": "core", "name": "start_epoch", "raw_value": "1727075266.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-26", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 26, "time_seconds": 33.95084881782532, "inputs": {"library|input_1": {"src": "hda", "id": "760b73d9d9f85dea"}, "library|input_2": {"src": "hda", "id": "0cd5123ee42adb8f"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "filter_options|minimum_length": "10", "filter_options|minimum_length2": "10", "filter_options|maximum_length": "50", "filter_options|pair_filter": "both"}, "job": {"model_class": "Job", "id": "20e650b6a023a7b1", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:43:09.279904", "update_time": "2024-09-23T06:43:22.961848", "galaxy_version": "24.1", "external_id": "gxy-7t8kz", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/d/3/dataset_5d308e69-ce66-435d-bd02-c515cfddecbd.dat' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/5/7/c/dataset_57c25415-32ba-44aa-bb73-f61c790aa8dc.dat' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10:10 --maximum-length=50 --pair-filter=both -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"50\", \"maximum_length2\": \"\", \"minimum_length\": \"10\", \"minimum_length2\": \"10\", \"pair_filter\": \"both\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 77, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 78, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "760b73d9d9f85dea", "src": "hda", "uuid": "5d308e69-ce66-435d-bd02-c515cfddecbd"}, "library|input_2": {"id": "0cd5123ee42adb8f", "src": "hda", "uuid": "57c25415-32ba-44aa-bb73-f61c790aa8dc"}}, "outputs": {"out1": {"id": "2f0778d0c0cf8c0e", "src": "hda", "uuid": "5ca3b808-78f8-49a8-af0a-2f9ca46c3fbd"}, "out2": {"id": "a4a06a8685c9ef3c", "src": "hda", "uuid": "cb07ddcc-2d3b-44fe-8ffc-1f9b36546ac8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10:10 --maximum-length=50 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.157 s (1590.543 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10:10 --maximum-length=50 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.157 s (1590.543 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:43:11", "plugin": "core", "name": "end_epoch", "raw_value": "1727073791.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:43:10", "plugin": "core", "name": "start_epoch", "raw_value": "1727073790.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-26", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 26, "time_seconds": 34.291109800338745, "inputs": {"library|input_1": {"src": "hda", "id": "e728fb252000105e"}, "library|input_2": {"src": "hda", "id": "77d432dca06c69ef"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "filter_options|minimum_length": "10", "filter_options|minimum_length2": "10", "filter_options|maximum_length": "50", "filter_options|pair_filter": "both"}, "job": {"model_class": "Job", "id": "1a6a5a224659a5e4", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:08:20.271532", "update_time": "2024-09-23T07:08:33.574232", "galaxy_version": "24.1", "external_id": "gxy-s6pd6", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/a/2/c/dataset_a2cb71d4-dbd9-4a5a-9fcf-bb6fe2c1d0a3.dat' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/7/7/0/dataset_770f93fb-e972-4017-8763-f23428f8ed16.dat' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10:10 --maximum-length=50 --pair-filter=both -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"50\", \"maximum_length2\": \"\", \"minimum_length\": \"10\", \"minimum_length2\": \"10\", \"pair_filter\": \"both\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 205, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 206, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "e728fb252000105e", "src": "hda", "uuid": "a2cb71d4-dbd9-4a5a-9fcf-bb6fe2c1d0a3"}, "library|input_2": {"id": "77d432dca06c69ef", "src": "hda", "uuid": "770f93fb-e972-4017-8763-f23428f8ed16"}}, "outputs": {"out1": {"id": "b9844a71c8f1ac4d", "src": "hda", "uuid": "4119c30e-81a7-4858-8ef1-b6becd736909"}, "out2": {"id": "f02143bb9ebff769", "src": "hda", "uuid": "0194c89a-8174-4952-bda4-079e88c74b11"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10:10 --maximum-length=50 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.156 s (1576.872 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=10:10 --maximum-length=50 --pair-filter=both -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.156 s (1576.872 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs that were too long: 96 (97.0%)\nPairs written (passing filters): 3 (3.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 99 bp (0.2%)\n Read 1: 51 bp\n Read 2: 48 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:08:22", "plugin": "core", "name": "end_epoch", "raw_value": "1727075302.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:08:22", "plugin": "core", "name": "start_epoch", "raw_value": "1727075302.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-27", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 27, "time_seconds": 33.729694843292236, "inputs": {"library|input_1": {"src": "hda", "id": "551e181a06b24949"}, "library|r1|adapters_0|adapter_source|adapter": "AGCCGCTANGACG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|shorten_options|length": "10", "other_trimming_options|shorten_options|shorten_end": "3prime", "other_trimming_options|shorten_options|shorten_values": "True", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "db928d5e388f7f4d", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:43:43.778498", "update_time": "2024-09-23T06:43:57.144024", "galaxy_version": "24.1", "external_id": "gxy-4crhv", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/7/b/7/dataset_7b745779-87b7-4a4f-8bf6-749a635c3e39.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGCCGCTANGACG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 0, \"length\": \"10\", \"shorten_end\": \"3prime\", \"shorten_values\": \"True\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 81, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCCGCTANGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "551e181a06b24949", "src": "hda", "uuid": "7b745779-87b7-4a4f-8bf6-749a635c3e39"}}, "outputs": {"out1": {"id": "3338b4d936bf5d7f", "src": "hda", "uuid": "d1fe4efc-be6a-4ac7-8732-689dca44aa3d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (13876.994 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 20 bp (19.6%)\n\n=== Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (13876.994 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 20 bp (19.6%)\n\n=== Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:43:46", "plugin": "core", "name": "end_epoch", "raw_value": "1727073826.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:43:45", "plugin": "core", "name": "start_epoch", "raw_value": "1727073825.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-27", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 27, "time_seconds": 34.703128814697266, "inputs": {"library|input_1": {"src": "hda", "id": "fec5d94b97744176"}, "library|r1|adapters_0|adapter_source|adapter": "AGCCGCTANGACG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|shorten_options|length": "10", "other_trimming_options|shorten_options|shorten_end": "3prime", "other_trimming_options|shorten_options|shorten_values": "True", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "b809a343ea227e66", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:08:54.923214", "update_time": "2024-09-23T07:09:08.779506", "galaxy_version": "24.1", "external_id": "gxy-g7xjs", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/7/f/b/dataset_7fb6d787-7ceb-4089-af6f-2ec311f25f8f.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGCCGCTANGACG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 0, \"length\": \"10\", \"shorten_end\": \"3prime\", \"shorten_values\": \"True\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 209, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCCGCTANGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "fec5d94b97744176", "src": "hda", "uuid": "7fb6d787-7ceb-4089-af6f-2ec311f25f8f"}}, "outputs": {"out1": {"id": "129d39eb88ca022b", "src": "hda", "uuid": "e74f3c58-3423-4f5b-bfd6-843c2b14579b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.049 s (16438.961 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 20 bp (19.6%)\n\n=== Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.049 s (16438.961 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 20 bp (19.6%)\n\n=== Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:08:57", "plugin": "core", "name": "end_epoch", "raw_value": "1727075337.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:08:56", "plugin": "core", "name": "start_epoch", "raw_value": "1727075336.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-28", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 28, "time_seconds": 34.504263162612915, "inputs": {"library|input_1": {"src": "hda", "id": "afd0db1207c12bbe"}, "library|r1|adapters_0|adapter_source|adapter": "AGCCGCTANGACG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|shorten_options|length": "10", "other_trimming_options|shorten_options|shorten_end": "5prime", "other_trimming_options|shorten_options|shorten_values": "True", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "25730af967443c99", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:44:17.932324", "update_time": "2024-09-23T06:44:31.765394", "galaxy_version": "24.1", "external_id": "gxy-7nnm5", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/f/2/3/dataset_f23959f3-29c9-4cd6-b8fd-15ed3ecb1d36.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGCCGCTANGACG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 0, \"length\": \"10\", \"shorten_end\": \"5prime\", \"shorten_values\": \"True\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 83, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCCGCTANGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "afd0db1207c12bbe", "src": "hda", "uuid": "f23959f3-29c9-4cd6-b8fd-15ed3ecb1d36"}}, "outputs": {"out1": {"id": "af659102835003e0", "src": "hda", "uuid": "ddf7fd82-f802-4ade-bc2d-a27cd50e9732"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14339.209 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 20 bp (19.6%)\n\n=== Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14339.209 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 20 bp (19.6%)\n\n=== Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:44:20", "plugin": "core", "name": "end_epoch", "raw_value": "1727073860.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:44:19", "plugin": "core", "name": "start_epoch", "raw_value": "1727073859.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-28", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 28, "time_seconds": 35.03817105293274, "inputs": {"library|input_1": {"src": "hda", "id": "2dcbbe31c83616e8"}, "library|r1|adapters_0|adapter_source|adapter": "AGCCGCTANGACG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|shorten_options|length": "10", "other_trimming_options|shorten_options|shorten_end": "5prime", "other_trimming_options|shorten_options|shorten_values": "True", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "6cf4c296eae030fb", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:09:29.404526", "update_time": "2024-09-23T07:09:44.020900", "galaxy_version": "24.1", "external_id": "gxy-gn7d2", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/3/1/9/dataset_319b03c5-3ef8-400b-af45-c08b902342df.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGCCGCTANGACG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 0, \"length\": \"10\", \"shorten_end\": \"5prime\", \"shorten_values\": \"True\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 211, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCCGCTANGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "2dcbbe31c83616e8", "src": "hda", "uuid": "319b03c5-3ef8-400b-af45-c08b902342df"}}, "outputs": {"out1": {"id": "5dda5717602a99bd", "src": "hda", "uuid": "764f3641-4aae-43a6-92dd-825e83f14598"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14253.696 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 20 bp (19.6%)\n\n=== Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14253.696 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 1 (33.3%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 20 bp (19.6%)\n\n=== Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:09:32", "plugin": "core", "name": "end_epoch", "raw_value": "1727075372.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:09:31", "plugin": "core", "name": "start_epoch", "raw_value": "1727075371.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-29", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 29, "time_seconds": 37.345168352127075, "inputs": {"library|input_1": {"src": "hda", "id": "eaf3cc95bfb04d40"}, "library|r1|adapters_0|adapter_source|adapter": "AGCCGCTANGACG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGCCGCTANGACG", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "other_trimming_options|shorten_options|length": "10", "other_trimming_options|shorten_options|shorten_end": "3prime", "other_trimming_options|shorten_options|shorten_values": "True", "other_trimming_options|shorten_options_r2|length2": "10", "other_trimming_options|shorten_options_r2|shorten_end_r2": "5prime", "other_trimming_options|shorten_options_r2|shorten_values_r2": "True", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "fc9418bd75c7a473", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:44:52.823133", "update_time": "2024-09-23T06:45:08.506474", "galaxy_version": "24.1", "external_id": "gxy-2j4xk", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/1/e/3/dataset_1e3f2880-4edf-4f9d-8bba-e9c937fcd7bf.dat' 'cutadapt_small_fastq_1.fq' && ln -f -s '/galaxy/server/database/objects/1/e/3/dataset_1e3f2880-4edf-4f9d-8bba-e9c937fcd7bf.dat' 'cutadapt_small_fastq_2.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGCCGCTANGACG' -A 'AGCCGCTANGACG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -L -10 -o 'out1.fq' -p 'out2.fq' 'cutadapt_small_fastq_1.fq' 'cutadapt_small_fastq_2.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 0, \"length\": \"10\", \"shorten_end\": \"3prime\", \"shorten_values\": \"True\"}, \"shorten_options_r2\": {\"__current_case__\": 0, \"length2\": \"10\", \"shorten_end_r2\": \"5prime\", \"shorten_values_r2\": \"True\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 85, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 85, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCCGCTANGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCCGCTANGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "eaf3cc95bfb04d40", "src": "hda", "uuid": "1e3f2880-4edf-4f9d-8bba-e9c937fcd7bf"}, "library|input_2": {"id": "eaf3cc95bfb04d40", "src": "hda", "uuid": "1e3f2880-4edf-4f9d-8bba-e9c937fcd7bf"}}, "outputs": {"out1": {"id": "fa2a3ff6aa62faab", "src": "hda", "uuid": "d73211e9-9839-4171-ba9b-733983fb3970"}, "out2": {"id": "82e4220b4afc8d32", "src": "hda", "uuid": "50df0693-78d1-4392-beb0-f353f889f299"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG -A AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -L -10 -o out1.fq -p out2.fq cutadapt_small_fastq_1.fq cutadapt_small_fastq_2.fq\nProcessing paired-end reads on 5 cores ...\nFinished in 0.061 s (20374.616 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 3\n Read 1 with adapter: 1 (33.3%)\n Read 2 with adapter: 1 (33.3%)\nPairs written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 204 bp\n Read 1: 102 bp\n Read 2: 102 bp\nTotal written (filtered): 40 bp (19.6%)\n Read 1: 20 bp\n Read 2: 20 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG -A AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -L -10 -o out1.fq -p out2.fq cutadapt_small_fastq_1.fq cutadapt_small_fastq_2.fq\nProcessing paired-end reads on 5 cores ...\nFinished in 0.061 s (20374.616 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 3\n Read 1 with adapter: 1 (33.3%)\n Read 2 with adapter: 1 (33.3%)\nPairs written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 204 bp\n Read 1: 102 bp\n Read 2: 102 bp\nTotal written (filtered): 40 bp (19.6%)\n Read 1: 20 bp\n Read 2: 20 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:44:55", "plugin": "core", "name": "end_epoch", "raw_value": "1727073895.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:44:55", "plugin": "core", "name": "start_epoch", "raw_value": "1727073895.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-29", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 29, "time_seconds": 34.423935413360596, "inputs": {"library|input_1": {"src": "hda", "id": "b005e3ff72c760ae"}, "library|r1|adapters_0|adapter_source|adapter": "AGCCGCTANGACG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGCCGCTANGACG", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "other_trimming_options|shorten_options|length": "10", "other_trimming_options|shorten_options|shorten_end": "3prime", "other_trimming_options|shorten_options|shorten_values": "True", "other_trimming_options|shorten_options_r2|length2": "10", "other_trimming_options|shorten_options_r2|shorten_end_r2": "5prime", "other_trimming_options|shorten_options_r2|shorten_values_r2": "True", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "583130bd74666373", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:10:03.900437", "update_time": "2024-09-23T07:10:17.838620", "galaxy_version": "24.1", "external_id": "gxy-hw6f8", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/8/2/a/dataset_82a201ef-83ad-4d8f-9f60-c2038a715a33.dat' 'cutadapt_small_fastq_1.fq' && ln -f -s '/galaxy/server/database/objects/8/2/a/dataset_82a201ef-83ad-4d8f-9f60-c2038a715a33.dat' 'cutadapt_small_fastq_2.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGCCGCTANGACG' -A 'AGCCGCTANGACG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -L -10 -o 'out1.fq' -p 'out2.fq' 'cutadapt_small_fastq_1.fq' 'cutadapt_small_fastq_2.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 0, \"length\": \"10\", \"shorten_end\": \"3prime\", \"shorten_values\": \"True\"}, \"shorten_options_r2\": {\"__current_case__\": 0, \"length2\": \"10\", \"shorten_end_r2\": \"5prime\", \"shorten_values_r2\": \"True\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 213, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 213, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCCGCTANGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCCGCTANGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "b005e3ff72c760ae", "src": "hda", "uuid": "82a201ef-83ad-4d8f-9f60-c2038a715a33"}, "library|input_2": {"id": "b005e3ff72c760ae", "src": "hda", "uuid": "82a201ef-83ad-4d8f-9f60-c2038a715a33"}}, "outputs": {"out1": {"id": "c79b33f10299ee40", "src": "hda", "uuid": "2f4c6e15-f38f-4f05-ac20-f39d27275ea4"}, "out2": {"id": "cb976c5007515b5b", "src": "hda", "uuid": "e914f9c7-786f-4f6f-8d1d-02d925d78b17"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG -A AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -L -10 -o out1.fq -p out2.fq cutadapt_small_fastq_1.fq cutadapt_small_fastq_2.fq\nProcessing paired-end reads on 5 cores ...\nFinished in 0.061 s (20307.223 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 3\n Read 1 with adapter: 1 (33.3%)\n Read 2 with adapter: 1 (33.3%)\nPairs written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 204 bp\n Read 1: 102 bp\n Read 2: 102 bp\nTotal written (filtered): 40 bp (19.6%)\n Read 1: 20 bp\n Read 2: 20 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCCGCTANGACG -A AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 -L -10 -o out1.fq -p out2.fq cutadapt_small_fastq_1.fq cutadapt_small_fastq_2.fq\nProcessing paired-end reads on 5 cores ...\nFinished in 0.061 s (20307.223 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 3\n Read 1 with adapter: 1 (33.3%)\n Read 2 with adapter: 1 (33.3%)\nPairs written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 204 bp\n Read 1: 102 bp\n Read 2: 102 bp\nTotal written (filtered): 40 bp (19.6%)\n Read 1: 20 bp\n Read 2: 20 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:10:06", "plugin": "core", "name": "end_epoch", "raw_value": "1727075406.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:10:05", "plugin": "core", "name": "start_epoch", "raw_value": "1727075405.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-3", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 3, "time_seconds": 35.93841886520386, "inputs": {"library|input_1": {"src": "hdca", "id": "abbc0a781ea0cf97"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired_collection"}, "job": {"model_class": "Job", "id": "6a9995029a212ee8", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:31:29.507227", "update_time": "2024-09-23T06:31:43.820070", "galaxy_version": "24.1", "external_id": "gxy-ws9dt", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/8/9/c/dataset_89c738ec-e54b-45b1-8b4a-b798313cb35d.dat' 'Unnamed Collection_1.fq.gz' && ln -f -s '/galaxy/server/database/objects/1/2/7/dataset_12707498-42d4-4da8-a3f0-8216ab21b401.dat' 'Unnamed Collection_2.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'Unnamed Collection_1.fq.gz' 'Unnamed Collection_2.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"library": "{\"__current_case__\": 2, \"input_1\": {\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired_collection\"}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "output_selector": null, "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"library|input_12": {"id": "6a9995029a212ee8", "src": "hda", "uuid": "12707498-42d4-4da8-a3f0-8216ab21b401"}, "library|input_11": {"id": "c5cf6b2dd288fef9", "src": "hda", "uuid": "89c738ec-e54b-45b1-8b4a-b798313cb35d"}}, "outputs": {"out_pairs|__part__|reverse": {"id": "60115470358eb9ac", "src": "hda", "uuid": "eb74da1f-1545-4604-913f-1f85b0489289"}, "out_pairs|__part__|forward": {"id": "c01ea000a8fa16a6", "src": "hda", "uuid": "fcf754cb-2760-44dd-85de-3697dfe63c62"}}, "copied_from_job_id": null, "output_collections": {"out_pairs": {"src": "hdca", "id": "c75fb1819c3bf55e"}}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.174 s (1753.116 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.174 s (1753.116 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:31:31", "plugin": "core", "name": "start_epoch", "raw_value": "1727073091.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:31:31", "plugin": "core", "name": "end_epoch", "raw_value": "1727073091.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-3", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 3, "time_seconds": 33.81545853614807, "inputs": {"library|input_1": {"src": "hdca", "id": "36226e39681520ef"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired_collection"}, "job": {"model_class": "Job", "id": "2eead06849c1ea73", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:56:31.110409", "update_time": "2024-09-23T06:56:44.518438", "galaxy_version": "24.1", "external_id": "gxy-wgnns", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/6/4/dataset_56455281-4d4c-440a-8ff3-4e934a85fe61.dat' 'Unnamed Collection_1.fq.gz' && ln -f -s '/galaxy/server/database/objects/c/1/1/dataset_c117a3f4-18f4-4087-8d17-c6f2337fb7ca.dat' 'Unnamed Collection_2.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'Unnamed Collection_1.fq.gz' 'Unnamed Collection_2.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 2, \"input_1\": {\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired_collection\"}"}, "inputs": {"library|input_11": {"id": "dfb1ed8629dfe572", "src": "hda", "uuid": "56455281-4d4c-440a-8ff3-4e934a85fe61"}, "library|input_12": {"id": "5575219d3af680b7", "src": "hda", "uuid": "c117a3f4-18f4-4087-8d17-c6f2337fb7ca"}}, "outputs": {"out_pairs|__part__|forward": {"id": "0e49637410094e1b", "src": "hda", "uuid": "2da215d2-a96c-4eea-80cb-200fe864de40"}, "out_pairs|__part__|reverse": {"id": "e1540c18cae3d976", "src": "hda", "uuid": "f74c2172-f998-4f7f-a0c0-fb090e426841"}}, "copied_from_job_id": null, "output_collections": {"out_pairs": {"src": "hdca", "id": "982abeb0f0360d8e"}}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.169 s (1708.052 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.169 s (1708.052 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:56:33", "plugin": "core", "name": "end_epoch", "raw_value": "1727074593.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:56:33", "plugin": "core", "name": "start_epoch", "raw_value": "1727074593.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-30", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 30, "time_seconds": 38.18690204620361, "inputs": {"library|input_1": {"src": "hda", "id": "acc4b2644dfe0281"}, "library|r2|adapters2_0|adapter_source|adapter": "AGCCGCTANGACG", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "other_trimming_options|shorten_options_r2|length2": "10", "other_trimming_options|shorten_options_r2|shorten_end_r2": "3prime", "other_trimming_options|shorten_options_r2|shorten_values_r2": "True", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "cb1d521ab1fd0bb6", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:45:32.007474", "update_time": "2024-09-23T06:45:46.897921", "galaxy_version": "24.1", "external_id": "gxy-k9lch", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/c/1/8/dataset_c1864908-7abc-4cf0-af7b-121e2ffb3893.dat' 'cutadapt_small_fastq_1.fq' && ln -f -s '/galaxy/server/database/objects/c/1/8/dataset_c1864908-7abc-4cf0-af7b-121e2ffb3893.dat' 'cutadapt_small_fastq_2.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -A 'AGCCGCTANGACG' --error-rate=0.1 --times=1 --overlap=3 --action=trim -L 10 -o 'out1.fq' -p 'out2.fq' 'cutadapt_small_fastq_1.fq' 'cutadapt_small_fastq_2.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 0, \"length2\": \"10\", \"shorten_end_r2\": \"3prime\", \"shorten_values_r2\": \"True\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 88, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 88, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCCGCTANGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "acc4b2644dfe0281", "src": "hda", "uuid": "c1864908-7abc-4cf0-af7b-121e2ffb3893"}, "library|input_2": {"id": "acc4b2644dfe0281", "src": "hda", "uuid": "c1864908-7abc-4cf0-af7b-121e2ffb3893"}}, "outputs": {"out1": {"id": "13f797ac29bd9428", "src": "hda", "uuid": "600b79cc-4c4b-4173-b4a1-cb2de670b3ad"}, "out2": {"id": "5d83015c579c9850", "src": "hda", "uuid": "f4298231-b69f-4511-956b-ab00d0486097"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -A AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim -L 10 -o out1.fq -p out2.fq cutadapt_small_fastq_1.fq cutadapt_small_fastq_2.fq\nProcessing paired-end reads on 5 cores ...\nFinished in 0.062 s (20696.640 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 3\n Read 2 with adapter: 1 (33.3%)\nPairs written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 204 bp\n Read 1: 102 bp\n Read 2: 102 bp\nTotal written (filtered): 122 bp (59.8%)\n Read 1: 102 bp\n Read 2: 20 bp\n\n=== Second read: Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -A AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim -L 10 -o out1.fq -p out2.fq cutadapt_small_fastq_1.fq cutadapt_small_fastq_2.fq\nProcessing paired-end reads on 5 cores ...\nFinished in 0.062 s (20696.640 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 3\n Read 2 with adapter: 1 (33.3%)\nPairs written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 204 bp\n Read 1: 102 bp\n Read 2: 102 bp\nTotal written (filtered): 122 bp (59.8%)\n Read 1: 102 bp\n Read 2: 20 bp\n\n=== Second read: Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:45:34", "plugin": "core", "name": "end_epoch", "raw_value": "1727073934.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:45:33", "plugin": "core", "name": "start_epoch", "raw_value": "1727073933.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-30", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 30, "time_seconds": 39.006020069122314, "inputs": {"library|input_1": {"src": "hda", "id": "6081f1a44ca61e97"}, "library|r2|adapters2_0|adapter_source|adapter": "AGCCGCTANGACG", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired", "other_trimming_options|shorten_options_r2|length2": "10", "other_trimming_options|shorten_options_r2|shorten_end_r2": "3prime", "other_trimming_options|shorten_options_r2|shorten_values_r2": "True", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "ee4b014024418022", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:10:43.038856", "update_time": "2024-09-23T07:10:56.839990", "galaxy_version": "24.1", "external_id": "gxy-rmx68", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/0/e/dataset_50e719f1-5837-47eb-bffa-9ff43acbdb01.dat' 'cutadapt_small_fastq_1.fq' && ln -f -s '/galaxy/server/database/objects/5/0/e/dataset_50e719f1-5837-47eb-bffa-9ff43acbdb01.dat' 'cutadapt_small_fastq_2.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -A 'AGCCGCTANGACG' --error-rate=0.1 --times=1 --overlap=3 --action=trim -L 10 -o 'out1.fq' -p 'out2.fq' 'cutadapt_small_fastq_1.fq' 'cutadapt_small_fastq_2.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 0, \"length2\": \"10\", \"shorten_end_r2\": \"3prime\", \"shorten_values_r2\": \"True\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 216, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 216, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCCGCTANGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "6081f1a44ca61e97", "src": "hda", "uuid": "50e719f1-5837-47eb-bffa-9ff43acbdb01"}, "library|input_2": {"id": "6081f1a44ca61e97", "src": "hda", "uuid": "50e719f1-5837-47eb-bffa-9ff43acbdb01"}}, "outputs": {"out1": {"id": "0faed797a64c6f5c", "src": "hda", "uuid": "d430ea04-4ecf-4910-9c27-15d84ef5f7dc"}, "out2": {"id": "69190c74664914bc", "src": "hda", "uuid": "e1e82f0c-6523-47d7-866c-63532cd38fa0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -A AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim -L 10 -o out1.fq -p out2.fq cutadapt_small_fastq_1.fq cutadapt_small_fastq_2.fq\nProcessing paired-end reads on 5 cores ...\nFinished in 0.048 s (16137.679 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 3\n Read 2 with adapter: 1 (33.3%)\nPairs written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 204 bp\n Read 1: 102 bp\n Read 2: 102 bp\nTotal written (filtered): 122 bp (59.8%)\n Read 1: 102 bp\n Read 2: 20 bp\n\n=== Second read: Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -A AGCCGCTANGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim -L 10 -o out1.fq -p out2.fq cutadapt_small_fastq_1.fq cutadapt_small_fastq_2.fq\nProcessing paired-end reads on 5 cores ...\nFinished in 0.048 s (16137.679 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 3\n Read 2 with adapter: 1 (33.3%)\nPairs written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 204 bp\n Read 1: 102 bp\n Read 2: 102 bp\nTotal written (filtered): 122 bp (59.8%)\n Read 1: 102 bp\n Read 2: 20 bp\n\n=== Second read: Adapter 1 ===\n\nSequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 0.0%\n none/other: 100.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n34\t1\t0.0\t1\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:10:45", "plugin": "core", "name": "end_epoch", "raw_value": "1727075445.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:10:45", "plugin": "core", "name": "start_epoch", "raw_value": "1727075445.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-31", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 31, "time_seconds": 36.27175998687744, "inputs": {"library|input_1": {"src": "hda", "id": "821c445288e7bcc0"}, "library|r1|adapters_0|adapter_source|adapter": "AGCGGCTTAGACG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "filter_options|max_expected_errors": "10"}, "job": {"model_class": "Job", "id": "d9035bff43c21374", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:46:09.679447", "update_time": "2024-09-23T06:46:23.978824", "galaxy_version": "24.1", "external_id": "gxy-28dzh", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/1/9/dataset_51994b2c-d1c0-4d0c-baec-17056bc95169.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGCGGCTTAGACG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --max-ee=10.0 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"10.0\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 91, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCGGCTTAGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "821c445288e7bcc0", "src": "hda", "uuid": "51994b2c-d1c0-4d0c-baec-17056bc95169"}}, "outputs": {"out1": {"id": "c73fce42c6ec59fa", "src": "hda", "uuid": "a00e3e95-633d-4cbe-9cc4-7f442251869b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCGGCTTAGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --max-ee=10.0 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.046 s (15224.059 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads with too many exp. errors: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGCGGCTTAGACG; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCGGCTTAGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --max-ee=10.0 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.046 s (15224.059 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads with too many exp. errors: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGCGGCTTAGACG; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:46:12", "plugin": "core", "name": "end_epoch", "raw_value": "1727073972.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:46:11", "plugin": "core", "name": "start_epoch", "raw_value": "1727073971.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-31", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 31, "time_seconds": 33.76112341880798, "inputs": {"library|input_1": {"src": "hda", "id": "b77e088473acf86f"}, "library|r1|adapters_0|adapter_source|adapter": "AGCGGCTTAGACG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "filter_options|max_expected_errors": "10"}, "job": {"model_class": "Job", "id": "a4acf38289516d5b", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:11:17.130613", "update_time": "2024-09-23T07:11:31.264974", "galaxy_version": "24.1", "external_id": "gxy-sbrg5", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/a/2/dataset_da226b70-22eb-4331-897d-e8d8d38db61a.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGCGGCTTAGACG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --max-ee=10.0 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"10.0\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 219, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGCGGCTTAGACG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "b77e088473acf86f", "src": "hda", "uuid": "da226b70-22eb-4331-897d-e8d8d38db61a"}}, "outputs": {"out1": {"id": "2a78b53ebc84fd37", "src": "hda", "uuid": "6a292f26-4acd-489d-a703-e7b52c8d11c5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCGGCTTAGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --max-ee=10.0 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.047 s (15829.484 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads with too many exp. errors: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGCGGCTTAGACG; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGCGGCTTAGACG --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --max-ee=10.0 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.047 s (15829.484 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads with too many exp. errors: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: AGCGGCTTAGACG; Type: regular 3'; Length: 13; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:11:20", "plugin": "core", "name": "end_epoch", "raw_value": "1727075480.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:11:19", "plugin": "core", "name": "start_epoch", "raw_value": "1727075479.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-32", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 32, "time_seconds": 34.25221061706543, "inputs": {"library|input_1": {"src": "hda", "id": "9a638e08ec1bb1c2"}, "library|r1|adapters_0|adapter_source|adapter": "GAANTAGCTACCACX", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single"}, "job": {"model_class": "Job", "id": "ad74905b0cba1fb9", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:46:44.676910", "update_time": "2024-09-23T06:46:58.379837", "galaxy_version": "24.1", "external_id": "gxy-qr8jp", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/0/5/d/dataset_05da01c0-90e1-4ae3-b0f0-3711d0f9035e.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'GAANTAGCTACCACX' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 93, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"GAANTAGCTACCACX\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "9a638e08ec1bb1c2", "src": "hda", "uuid": "05da01c0-90e1-4ae3-b0f0-3711d0f9035e"}}, "outputs": {"out1": {"id": "3a372cbd9ed2e1e9", "src": "hda", "uuid": "32e53ce9-9883-47bc-acb5-560519c95425"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a GAANTAGCTACCACX --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (14146.884 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: GAANTAGCTACCAC; Type: non-internal 3'; Length: 14; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a GAANTAGCTACCACX --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (14146.884 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: GAANTAGCTACCAC; Type: non-internal 3'; Length: 14; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:46:46", "plugin": "core", "name": "end_epoch", "raw_value": "1727074006.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:46:46", "plugin": "core", "name": "start_epoch", "raw_value": "1727074006.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-32", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 32, "time_seconds": 32.557371854782104, "inputs": {"library|input_1": {"src": "hda", "id": "49adb5f856bc6730"}, "library|r1|adapters_0|adapter_source|adapter": "GAANTAGCTACCACX", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single"}, "job": {"model_class": "Job", "id": "7cdb4df5cdd75b45", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:11:51.207042", "update_time": "2024-09-23T07:12:04.066387", "galaxy_version": "24.1", "external_id": "gxy-4nzl8", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/a/5/2/dataset_a523ccc6-c698-462e-a245-0006b83319ac.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'GAANTAGCTACCACX' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 221, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"GAANTAGCTACCACX\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "49adb5f856bc6730", "src": "hda", "uuid": "a523ccc6-c698-462e-a245-0006b83319ac"}}, "outputs": {"out1": {"id": "463ab6aaed89beca", "src": "hda", "uuid": "1147a894-b35d-42f8-88ed-04870dff6715"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a GAANTAGCTACCACX --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (13643.185 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: GAANTAGCTACCAC; Type: non-internal 3'; Length: 14; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a GAANTAGCTACCACX --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (13643.185 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 0 (0.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 102 bp (100.0%)\n\n=== Adapter 1 ===\n\nSequence: GAANTAGCTACCAC; Type: non-internal 3'; Length: 14; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:11:53", "plugin": "core", "name": "end_epoch", "raw_value": "1727075513.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:11:52", "plugin": "core", "name": "start_epoch", "raw_value": "1727075512.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-33", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 33, "time_seconds": 36.28009510040283, "inputs": {"library|input_1": {"src": "hda", "id": "817d2151bdbc4e9a"}, "library|input_2": {"src": "hda", "id": "d6fa7b09a72b3483"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGCX", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGCX", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired"}, "job": {"model_class": "Job", "id": "0cd5123ee42adb8f", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:47:20.165125", "update_time": "2024-09-23T06:47:34.185719", "galaxy_version": "24.1", "external_id": "gxy-t9cc9", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/f/4/8/dataset_f48bd543-af9f-4262-ae6e-da18cafceb2f.dat' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/a/7/7/dataset_a7765045-4537-48de-8541-11d0b0034401.dat' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGCX' -A 'AGATCGGAAGAGCX' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_assimetric_fq_gz.fq.gz' 'bwa-mem-fastq2_assimetric_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 95, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 96, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGCX\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGCX\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "817d2151bdbc4e9a", "src": "hda", "uuid": "f48bd543-af9f-4262-ae6e-da18cafceb2f"}, "library|input_2": {"id": "d6fa7b09a72b3483", "src": "hda", "uuid": "a7765045-4537-48de-8541-11d0b0034401"}}, "outputs": {"out1": {"id": "3de64f972679a4bf", "src": "hda", "uuid": "3a2f3848-d361-482c-ad0e-b0c9a5613453"}, "out2": {"id": "786aac8009e2906b", "src": "hda", "uuid": "07fef72b-9050-451e-a49b-4151a334d1c8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGCX -A AGATCGGAAGAGCX --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.174 s (1758.130 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 48,270 bp (100.0%)\n Read 1: 24,141 bp\n Read 2: 24,129 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: non-internal 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: non-internal 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGCX -A AGATCGGAAGAGCX --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.174 s (1758.130 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 48,291 bp\n Read 1: 24,147 bp\n Read 2: 24,144 bp\nTotal written (filtered): 48,270 bp (100.0%)\n Read 1: 24,141 bp\n Read 2: 24,129 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: non-internal 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: non-internal 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:47:23", "plugin": "core", "name": "end_epoch", "raw_value": "1727074043.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:47:22", "plugin": "core", "name": "start_epoch", "raw_value": "1727074042.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-33", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 33, "time_seconds": 11.68388557434082, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "cutadapt/4.9+galaxy1-34", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 34, "status": "skip"}}, {"id": "cutadapt/4.9+galaxy1-34", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 34, "status": "skip"}}, {"id": "cutadapt/4.9+galaxy1-35", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 35, "time_seconds": 36.03833055496216, "inputs": {"library|input_1": {"src": "hdca", "id": "78731c6a5c429418"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r1|adapters_0|single_noindels": true, "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|single_noindels": true, "library|type": "paired_collection"}, "job": {"model_class": "Job", "id": "551e181a06b24949", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:47:56.040759", "update_time": "2024-09-23T06:48:10.605496", "galaxy_version": "24.1", "external_id": "gxy-87nkq", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/9/b/f/dataset_9bfcf655-b1af-40e0-92c2-5c4e57113ab8.dat' 'Unnamed Collection_1.fq.gz' && ln -f -s '/galaxy/server/database/objects/6/7/0/dataset_6704d901-3137-450b-b716-4b3f3ff28f51.dat' 'Unnamed Collection_2.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC;noindels' -A 'AGATCGGAAGAGC;noindels' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'Unnamed Collection_1.fq.gz' 'Unnamed Collection_2.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 2, \"input_1\": {\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": true}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": true}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired_collection\"}"}, "inputs": {"library|input_11": {"id": "7eb981d2085bfd9e", "src": "hda", "uuid": "9bfcf655-b1af-40e0-92c2-5c4e57113ab8"}, "library|input_12": {"id": "3850a7ba825114ab", "src": "hda", "uuid": "6704d901-3137-450b-b716-4b3f3ff28f51"}}, "outputs": {"out_pairs|__part__|forward": {"id": "300c12adb70eaab7", "src": "hda", "uuid": "e740caca-cb35-465f-b65e-e36a6b24e60e"}, "out_pairs|__part__|reverse": {"id": "5e9c992acf068709", "src": "hda", "uuid": "5ba92832-d096-4d91-af6f-9c29cbde925f"}}, "copied_from_job_id": null, "output_collections": {"out_pairs": {"src": "hdca", "id": "5bb4b82a19d7f1fd"}}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC;noindels -A AGATCGGAAGAGC;noindels --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.174 s (1753.073 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC;noindels -A AGATCGGAAGAGC;noindels --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.174 s (1753.073 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:47:59", "plugin": "core", "name": "end_epoch", "raw_value": "1727074079.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:47:58", "plugin": "core", "name": "start_epoch", "raw_value": "1727074078.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-35", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 35, "time_seconds": 34.79808807373047, "inputs": {"library|input_1": {"src": "hdca", "id": "6a9995029a212ee8"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r1|adapters_0|single_noindels": true, "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|single_noindels": true, "library|type": "paired_collection"}, "job": {"model_class": "Job", "id": "f96a7e5905955441", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:12:37.045904", "update_time": "2024-09-23T07:12:50.663226", "galaxy_version": "24.1", "external_id": "gxy-z8x94", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/a/b/1/dataset_ab1e53e6-920a-42ee-bec1-cc2682e6d7b6.dat' 'Unnamed Collection_1.fq.gz' && ln -f -s '/galaxy/server/database/objects/6/6/c/dataset_66ce0620-52a0-4dd1-a272-3c3e17ce4c39.dat' 'Unnamed Collection_2.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC;noindels' -A 'AGATCGGAAGAGC;noindels' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'Unnamed Collection_1.fq.gz' 'Unnamed Collection_2.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 2, \"input_1\": {\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": true}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": true}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired_collection\"}"}, "inputs": {"library|input_11": {"id": "810778576ec9a2e4", "src": "hda", "uuid": "ab1e53e6-920a-42ee-bec1-cc2682e6d7b6"}, "library|input_12": {"id": "f25e97603549590f", "src": "hda", "uuid": "66ce0620-52a0-4dd1-a272-3c3e17ce4c39"}}, "outputs": {"out_pairs|__part__|forward": {"id": "9e3f9bfea79b9451", "src": "hda", "uuid": "f81fd766-46fa-42e9-a982-9a1a39c29669"}, "out_pairs|__part__|reverse": {"id": "250d208160e778e4", "src": "hda", "uuid": "01f939c2-3d45-4ebb-8b2f-3cccdf84a514"}}, "copied_from_job_id": null, "output_collections": {"out_pairs": {"src": "hdca", "id": "c01ea000a8fa16a6"}}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC;noindels -A AGATCGGAAGAGC;noindels --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.173 s (1744.157 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC;noindels -A AGATCGGAAGAGC;noindels --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.173 s (1744.157 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 4 (4.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,677 bp (100.0%)\n Read 1: 24,843 bp\n Read 2: 24,834 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 50.0%\n T: 50.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n4\t1\t0.4\t0\t1\n5\t1\t0.1\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:12:39", "plugin": "core", "name": "end_epoch", "raw_value": "1727075559.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:12:39", "plugin": "core", "name": "start_epoch", "raw_value": "1727075559.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-36", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 36, "time_seconds": 35.39700698852539, "inputs": {"library|input_1": {"src": "hdca", "id": "4851fe9e1c1e44c5"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired_collection", "other_trimming_options|quality_cutoff": "5", "other_trimming_options|quality_cutoff2": "15,20"}, "job": {"model_class": "Job", "id": "af659102835003e0", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:48:31.890940", "update_time": "2024-09-23T06:48:46.156012", "galaxy_version": "24.1", "external_id": "gxy-55w47", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/4/b/9/dataset_4b920a2c-04eb-4135-bdd3-9171065540f1.dat' 'Unnamed Collection_1.fq.gz' && ln -f -s '/galaxy/server/database/objects/e/3/6/dataset_e36aed3d-24fb-4156-98a2-1030376db68c.dat' 'Unnamed Collection_2.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=5 -Q 15,20 --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'Unnamed Collection_1.fq.gz' 'Unnamed Collection_2.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"5\", \"quality_cutoff2\": \"15,20\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 2, \"input_1\": {\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired_collection\"}"}, "inputs": {"library|input_11": {"id": "50eab474c7f1170d", "src": "hda", "uuid": "4b920a2c-04eb-4135-bdd3-9171065540f1"}, "library|input_12": {"id": "eb7e127eed7d1bd3", "src": "hda", "uuid": "e36aed3d-24fb-4156-98a2-1030376db68c"}}, "outputs": {"out_pairs|__part__|forward": {"id": "98041e0b7758fa35", "src": "hda", "uuid": "47ca3084-fb65-4ec0-bd92-14094aaa20ce"}, "out_pairs|__part__|reverse": {"id": "8ae3fe9b5c661171", "src": "hda", "uuid": "fd1bae74-b1e4-45cb-9934-8907324ecb84"}}, "copied_from_job_id": null, "output_collections": {"out_pairs": {"src": "hdca", "id": "1d9a06d3201fe113"}}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=5 -Q 15,20 --minimum-length=1 -o out1.fq.gz -p out2.fq.gz Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.171 s (1731.391 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nQuality-trimmed: 747 bp (1.5%)\n Read 1: 0 bp\n Read 2: 747 bp\nTotal written (filtered): 48,938 bp (98.5%)\n Read 1: 24,843 bp\n Read 2: 24,095 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 100.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t1\t1.5\t0\t1\n4\t1\t0.4\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=5 -Q 15,20 --minimum-length=1 -o out1.fq.gz -p out2.fq.gz Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.171 s (1731.391 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 2 (2.0%)\n Read 2 with adapter: 2 (2.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nQuality-trimmed: 747 bp (1.5%)\n Read 1: 0 bp\n Read 2: 747 bp\nTotal written (filtered): 48,938 bp (98.5%)\n Read 1: 24,843 bp\n Read 2: 24,095 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 50.0%\n G: 50.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t2\t1.5\t0\t2\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 100.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t1\t1.5\t0\t1\n4\t1\t0.4\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:48:34", "plugin": "core", "name": "end_epoch", "raw_value": "1727074114.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:48:33", "plugin": "core", "name": "start_epoch", "raw_value": "1727074113.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-36", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 36, "time_seconds": 11.287839889526367, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "cutadapt/4.9+galaxy1-37", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 37, "time_seconds": 34.97058582305908, "inputs": {"library|input_1": {"src": "hdca", "id": "d3b28d6e0b2a0e29"}, "library|type": "paired_collection", "other_trimming_options|poly_a": true}, "job": {"model_class": "Job", "id": "82e4220b4afc8d32", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:49:07.565717", "update_time": "2024-09-23T06:49:21.115536", "galaxy_version": "24.1", "external_id": "gxy-7rg85", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/4/7/4/dataset_47416628-e130-4668-8ef9-bfae81a08921.dat' 'Unnamed Collection_1.fa' && ln -f -s '/galaxy/server/database/objects/0/e/5/dataset_0e581202-df03-42da-b98a-e64232dd44ff.dat' 'Unnamed Collection_2.fa' && cutadapt -j=${GALAXY_SLOTS:-4} --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o 'out1.fa' -p 'out2.fa' 'Unnamed Collection_1.fa' 'Unnamed Collection_2.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": true, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 2, \"input_1\": {\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired_collection\"}"}, "inputs": {"library|input_11": {"id": "c90661f331458e68", "src": "hda", "uuid": "47416628-e130-4668-8ef9-bfae81a08921"}, "library|input_12": {"id": "8549636690d6da7a", "src": "hda", "uuid": "0e581202-df03-42da-b98a-e64232dd44ff"}}, "outputs": {"out_pairs|__part__|forward": {"id": "060ca00062cc2f70", "src": "hda", "uuid": "c5272f81-1a26-426f-b0be-37e40a6e9927"}, "out_pairs|__part__|reverse": {"id": "af09ce9fbd8e19d4", "src": "hda", "uuid": "d884764d-1e39-4e63-80c6-5d283ed30ae7"}}, "copied_from_job_id": null, "output_collections": {"out_pairs": {"src": "hdca", "id": "4ec27651e3eeecb9"}}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o out1.fa -p out2.fa Unnamed Collection_1.fa Unnamed Collection_2.fa\nProcessing paired-end reads on 5 cores ...\nFinished in 0.042 s (10582.387 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 4\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 369 bp\n Read 1: 194 bp\n Read 2: 175 bp\nPoly-A-trimmed: 168 bp (45.5%)\n Read 1: 84 bp\n Read 2: 84 bp\nTotal written (filtered): 201 bp (54.5%)\n Read 1: 110 bp\n Read 2: 91 bp\n\n=== R1 poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n\n\n=== R2 poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o out1.fa -p out2.fa Unnamed Collection_1.fa Unnamed Collection_2.fa\nProcessing paired-end reads on 5 cores ...\nFinished in 0.042 s (10582.387 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 4\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 369 bp\n Read 1: 194 bp\n Read 2: 175 bp\nPoly-A-trimmed: 168 bp (45.5%)\n Read 1: 84 bp\n Read 2: 84 bp\nTotal written (filtered): 201 bp (54.5%)\n Read 1: 110 bp\n Read 2: 91 bp\n\n=== R1 poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n\n\n=== R2 poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:49:09", "plugin": "core", "name": "end_epoch", "raw_value": "1727074149.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:49:09", "plugin": "core", "name": "start_epoch", "raw_value": "1727074149.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-37", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 37, "time_seconds": 34.79894280433655, "inputs": {"library|input_1": {"src": "hdca", "id": "60115470358eb9ac"}, "library|type": "paired_collection", "other_trimming_options|poly_a": true}, "job": {"model_class": "Job", "id": "54ec7c8897e748ef", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:13:23.636517", "update_time": "2024-09-23T07:13:36.742092", "galaxy_version": "24.1", "external_id": "gxy-7h7vf", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/e/d/dataset_5ed35389-2ef9-49e1-a74d-04cd60e10fac.dat' 'Unnamed Collection_1.fa' && ln -f -s '/galaxy/server/database/objects/8/4/3/dataset_843d5b7a-41b4-493d-b301-71bd11028dc7.dat' 'Unnamed Collection_2.fa' && cutadapt -j=${GALAXY_SLOTS:-4} --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o 'out1.fa' -p 'out2.fa' 'Unnamed Collection_1.fa' 'Unnamed Collection_2.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": true, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 2, \"input_1\": {\"values\": [{\"id\": 16, \"src\": \"hdca\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired_collection\"}"}, "inputs": {"library|input_11": {"id": "c69fa4595c971c31", "src": "hda", "uuid": "5ed35389-2ef9-49e1-a74d-04cd60e10fac"}, "library|input_12": {"id": "5c71d2835951f7f7", "src": "hda", "uuid": "843d5b7a-41b4-493d-b301-71bd11028dc7"}}, "outputs": {"out_pairs|__part__|forward": {"id": "29c0d8f6b7eac41c", "src": "hda", "uuid": "c11cac81-a0ed-4688-bb21-4d2b38c9e48e"}, "out_pairs|__part__|reverse": {"id": "c7fe15621a9f268d", "src": "hda", "uuid": "60678079-f289-4086-bff8-ab617c309fac"}}, "copied_from_job_id": null, "output_collections": {"out_pairs": {"src": "hdca", "id": "c17966a0831dcc16"}}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o out1.fa -p out2.fa Unnamed Collection_1.fa Unnamed Collection_2.fa\nProcessing paired-end reads on 5 cores ...\nFinished in 0.042 s (10456.026 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 4\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 369 bp\n Read 1: 194 bp\n Read 2: 175 bp\nPoly-A-trimmed: 168 bp (45.5%)\n Read 1: 84 bp\n Read 2: 84 bp\nTotal written (filtered): 201 bp (54.5%)\n Read 1: 110 bp\n Read 2: 91 bp\n\n=== R1 poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n\n\n=== R2 poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o out1.fa -p out2.fa Unnamed Collection_1.fa Unnamed Collection_2.fa\nProcessing paired-end reads on 5 cores ...\nFinished in 0.042 s (10456.026 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 4\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 369 bp\n Read 1: 194 bp\n Read 2: 175 bp\nPoly-A-trimmed: 168 bp (45.5%)\n Read 1: 84 bp\n Read 2: 84 bp\nTotal written (filtered): 201 bp (54.5%)\n Read 1: 110 bp\n Read 2: 91 bp\n\n=== R1 poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n\n\n=== R2 poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:13:26", "plugin": "core", "name": "end_epoch", "raw_value": "1727075606.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:13:25", "plugin": "core", "name": "start_epoch", "raw_value": "1727075605.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-38", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 38, "time_seconds": 34.65878677368164, "inputs": {"library|input_1": {"src": "hda", "id": "dc9e43d48fae261a"}, "library|r1|adapters_0|adapter_source|adapter": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|overlap": "10"}, "job": {"model_class": "Job", "id": "13f797ac29bd9428", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:49:42.596636", "update_time": "2024-09-23T06:49:56.042891", "galaxy_version": "24.1", "external_id": "gxy-82zhj", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/a/7/5/dataset_a75307cf-6634-4373-8eda-9aa8ba17693c.dat' 'polya_1_fasta.fa' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA' --error-rate=0.1 --times=1 --overlap=10 --action=trim --minimum-length=1 -o 'out1.fa' 'polya_1_fasta.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"10\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 111, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "dc9e43d48fae261a", "src": "hda", "uuid": "a75307cf-6634-4373-8eda-9aa8ba17693c"}}, "outputs": {"out1": {"id": "e7f405730f7b4109", "src": "hda", "uuid": "db3973bd-ee90-4d8f-866b-ca0aba5629c6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --error-rate=0.1 --times=1 --overlap=10 --action=trim --minimum-length=1 -o out1.fa polya_1_fasta.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.044 s (11038.721 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 4\nReads with adapters: 3 (75.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 194 bp\nTotal written (filtered): 96 bp (49.5%)\n\n=== Adapter 1 ===\n\nSequence: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA; Type: regular 3'; Length: 35; Trimmed: 3 times\n\nMinimum overlap: 10\nNo. of allowed errors:\n1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-35 bp: 3\n\nBases preceding removed adapters:\n A: 0.0%\n C: 33.3%\n G: 66.7%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n26\t1\t0.0\t2\t0 0 1\n30\t1\t0.0\t3\t0 0 0 1\n42\t1\t0.0\t3\t0 1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --error-rate=0.1 --times=1 --overlap=10 --action=trim --minimum-length=1 -o out1.fa polya_1_fasta.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.044 s (11038.721 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 4\nReads with adapters: 3 (75.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 194 bp\nTotal written (filtered): 96 bp (49.5%)\n\n=== Adapter 1 ===\n\nSequence: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA; Type: regular 3'; Length: 35; Trimmed: 3 times\n\nMinimum overlap: 10\nNo. of allowed errors:\n1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-35 bp: 3\n\nBases preceding removed adapters:\n A: 0.0%\n C: 33.3%\n G: 66.7%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n26\t1\t0.0\t2\t0 0 1\n30\t1\t0.0\t3\t0 0 0 1\n42\t1\t0.0\t3\t0 1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:49:45", "plugin": "core", "name": "end_epoch", "raw_value": "1727074185.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:49:45", "plugin": "core", "name": "start_epoch", "raw_value": "1727074185.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-38", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 38, "time_seconds": 10.96432900428772, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "cutadapt/4.9+galaxy1-39", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 39, "time_seconds": 33.45357036590576, "inputs": {"library|input_1": {"src": "hda", "id": "fe9fd1ab37024b2e"}, "library|r1|adapters_0|adapter_source|adapter": "A{35}", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|overlap": "10"}, "job": {"model_class": "Job", "id": "821c445288e7bcc0", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:50:15.914942", "update_time": "2024-09-23T06:50:29.489830", "galaxy_version": "24.1", "external_id": "gxy-2b697", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/f/9/b/dataset_f9b23552-9553-41b3-9a51-4d92463161f6.dat' 'polya_1_fasta.fa' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'A{35}' --error-rate=0.1 --times=1 --overlap=10 --action=trim --minimum-length=1 -o 'out1.fa' 'polya_1_fasta.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"10\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 113, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"A{35}\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "fe9fd1ab37024b2e", "src": "hda", "uuid": "f9b23552-9553-41b3-9a51-4d92463161f6"}}, "outputs": {"out1": {"id": "3aae38a2b2c3bea2", "src": "hda", "uuid": "51bdfe5e-d278-4cbe-ba92-4d26ba72d972"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a A{35} --error-rate=0.1 --times=1 --overlap=10 --action=trim --minimum-length=1 -o out1.fa polya_1_fasta.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.044 s (10985.434 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 4\nReads with adapters: 3 (75.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 194 bp\nTotal written (filtered): 96 bp (49.5%)\n\n=== Adapter 1 ===\n\nSequence: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA; Type: regular 3'; Length: 35; Trimmed: 3 times\n\nMinimum overlap: 10\nNo. of allowed errors:\n1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-35 bp: 3\n\nBases preceding removed adapters:\n A: 0.0%\n C: 33.3%\n G: 66.7%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n26\t1\t0.0\t2\t0 0 1\n30\t1\t0.0\t3\t0 0 0 1\n42\t1\t0.0\t3\t0 1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a A{35} --error-rate=0.1 --times=1 --overlap=10 --action=trim --minimum-length=1 -o out1.fa polya_1_fasta.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.044 s (10985.434 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 4\nReads with adapters: 3 (75.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 194 bp\nTotal written (filtered): 96 bp (49.5%)\n\n=== Adapter 1 ===\n\nSequence: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA; Type: regular 3'; Length: 35; Trimmed: 3 times\n\nMinimum overlap: 10\nNo. of allowed errors:\n1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-35 bp: 3\n\nBases preceding removed adapters:\n A: 0.0%\n C: 33.3%\n G: 66.7%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n26\t1\t0.0\t2\t0 0 1\n30\t1\t0.0\t3\t0 0 0 1\n42\t1\t0.0\t3\t0 1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:50:18", "plugin": "core", "name": "end_epoch", "raw_value": "1727074218.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:50:17", "plugin": "core", "name": "start_epoch", "raw_value": "1727074217.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-39", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 39, "time_seconds": 33.64501667022705, "inputs": {"library|input_1": {"src": "hda", "id": "1e1db0cdd2dff83d"}, "library|r1|adapters_0|adapter_source|adapter": "A{35}", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|overlap": "10"}, "job": {"model_class": "Job", "id": "a169e5c8dd9d4e17", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:14:07.856935", "update_time": "2024-09-23T07:14:21.588495", "galaxy_version": "24.1", "external_id": "gxy-nk65x", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/9/e/0/dataset_9e058820-e2b8-4f7b-8b1b-fcf6ead3c2d3.dat' 'polya_1_fasta.fa' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'A{35}' --error-rate=0.1 --times=1 --overlap=10 --action=trim --minimum-length=1 -o 'out1.fa' 'polya_1_fasta.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"10\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 236, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"A{35}\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "1e1db0cdd2dff83d", "src": "hda", "uuid": "9e058820-e2b8-4f7b-8b1b-fcf6ead3c2d3"}}, "outputs": {"out1": {"id": "272286992fb506bb", "src": "hda", "uuid": "2d6e5b16-c911-4607-afa5-e78daec197a6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a A{35} --error-rate=0.1 --times=1 --overlap=10 --action=trim --minimum-length=1 -o out1.fa polya_1_fasta.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (10355.949 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 4\nReads with adapters: 3 (75.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 194 bp\nTotal written (filtered): 96 bp (49.5%)\n\n=== Adapter 1 ===\n\nSequence: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA; Type: regular 3'; Length: 35; Trimmed: 3 times\n\nMinimum overlap: 10\nNo. of allowed errors:\n1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-35 bp: 3\n\nBases preceding removed adapters:\n A: 0.0%\n C: 33.3%\n G: 66.7%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n26\t1\t0.0\t2\t0 0 1\n30\t1\t0.0\t3\t0 0 0 1\n42\t1\t0.0\t3\t0 1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a A{35} --error-rate=0.1 --times=1 --overlap=10 --action=trim --minimum-length=1 -o out1.fa polya_1_fasta.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (10355.949 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 4\nReads with adapters: 3 (75.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 194 bp\nTotal written (filtered): 96 bp (49.5%)\n\n=== Adapter 1 ===\n\nSequence: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA; Type: regular 3'; Length: 35; Trimmed: 3 times\n\nMinimum overlap: 10\nNo. of allowed errors:\n1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-35 bp: 3\n\nBases preceding removed adapters:\n A: 0.0%\n C: 33.3%\n G: 66.7%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n26\t1\t0.0\t2\t0 0 1\n30\t1\t0.0\t3\t0 0 0 1\n42\t1\t0.0\t3\t0 1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:14:10", "plugin": "core", "name": "end_epoch", "raw_value": "1727075650.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:14:10", "plugin": "core", "name": "start_epoch", "raw_value": "1727075650.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-4", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 4, "status": "skip"}}, {"id": "cutadapt/4.9+galaxy1-4", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 4, "status": "skip"}}, {"id": "cutadapt/4.9+galaxy1-40", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 40, "time_seconds": 33.065810203552246, "inputs": {"library|input_1": {"src": "hda", "id": "2b3d23383ab42ae7"}, "library|type": "single", "other_trimming_options|poly_a": true}, "job": {"model_class": "Job", "id": "9a638e08ec1bb1c2", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:50:49.692902", "update_time": "2024-09-23T06:51:02.717883", "galaxy_version": "24.1", "external_id": "gxy-mqrxc", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/f/f/8/dataset_ff8f5272-9111-45d1-8465-619024e1efd1.dat' 'polya_1_fasta.fa' && cutadapt -j=${GALAXY_SLOTS:-4} --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o 'out1.fa' 'polya_1_fasta.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": true, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 115, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "2b3d23383ab42ae7", "src": "hda", "uuid": "ff8f5272-9111-45d1-8465-619024e1efd1"}}, "outputs": {"out1": {"id": "9655f0b6eefaf9e7", "src": "hda", "uuid": "edfedf21-d186-4354-9537-82ab466c689f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o out1.fa polya_1_fasta.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.034 s (8619.130 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 4\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 194 bp\nPoly-A-trimmed: 84 bp (43.3%)\nTotal written (filtered): 110 bp (56.7%)\n\n=== Poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o out1.fa polya_1_fasta.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.034 s (8619.130 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 4\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 194 bp\nPoly-A-trimmed: 84 bp (43.3%)\nTotal written (filtered): 110 bp (56.7%)\n\n=== Poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:50:51", "plugin": "core", "name": "end_epoch", "raw_value": "1727074251.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:50:51", "plugin": "core", "name": "start_epoch", "raw_value": "1727074251.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-40", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 40, "time_seconds": 32.90908908843994, "inputs": {"library|input_1": {"src": "hda", "id": "3c9305a78b253272"}, "library|type": "single", "other_trimming_options|poly_a": true}, "job": {"model_class": "Job", "id": "e269aaa33e700c1d", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:14:41.903668", "update_time": "2024-09-23T07:14:54.618107", "galaxy_version": "24.1", "external_id": "gxy-kd79j", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/8/2/9/dataset_829603eb-1476-461a-8476-17ad1dfabfc9.dat' 'polya_1_fasta.fa' && cutadapt -j=${GALAXY_SLOTS:-4} --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o 'out1.fa' 'polya_1_fasta.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": true, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 238, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "3c9305a78b253272", "src": "hda", "uuid": "829603eb-1476-461a-8476-17ad1dfabfc9"}}, "outputs": {"out1": {"id": "8da721664896e4d3", "src": "hda", "uuid": "57cc3782-a069-4a97-a77b-90f3ccd61dc7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o out1.fa polya_1_fasta.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.032 s (8042.812 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 4\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 194 bp\nPoly-A-trimmed: 84 bp (43.3%)\nTotal written (filtered): 110 bp (56.7%)\n\n=== Poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --poly-a --minimum-length=1 -o out1.fa polya_1_fasta.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.032 s (8042.812 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 4\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 4 (100.0%)\n\nTotal basepairs processed: 194 bp\nPoly-A-trimmed: 84 bp (43.3%)\nTotal written (filtered): 110 bp (56.7%)\n\n=== Poly-A trimmed ===\n\nlength\tcount\n0\t1\n21\t2\n42\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:14:43", "plugin": "core", "name": "end_epoch", "raw_value": "1727075683.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:14:43", "plugin": "core", "name": "start_epoch", "raw_value": "1727075683.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-41", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 41, "time_seconds": 32.90667462348938, "inputs": {"library|input_1": {"src": "hda", "id": "2eead06849c1ea73"}, "library|type": "single"}, "job": {"model_class": "Job", "id": "817d2151bdbc4e9a", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:51:22.077411", "update_time": "2024-09-23T06:51:35.781169", "galaxy_version": "24.1", "external_id": "gxy-fzwx7", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/b/6/f/dataset_b6f533c5-05bf-4e68-ba7f-6740b449b3a2.dat' 'simple_fasta_gz.fa.gz' && cutadapt -j=${GALAXY_SLOTS:-4} --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fa.gz' 'simple_fasta_gz.fa.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 117, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "2eead06849c1ea73", "src": "hda", "uuid": "b6f533c5-05bf-4e68-ba7f-6740b449b3a2"}}, "outputs": {"out1": {"id": "fdc095a9f3fc5c3c", "src": "hda", "uuid": "a584b949-a138-46b4-9d8a-c63b0cbe61a4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fa.gz simple_fasta_gz.fa.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.087 s (43394.208 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 18 bp\nTotal written (filtered): 18 bp (100.0%)\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fa.gz simple_fasta_gz.fa.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.087 s (43394.208 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 18 bp\nTotal written (filtered): 18 bp (100.0%)\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 06:51:24", "plugin": "core", "name": "end_epoch", "raw_value": "1727074284.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:51:24", "plugin": "core", "name": "start_epoch", "raw_value": "1727074284.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-41", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 41, "time_seconds": 34.396857261657715, "inputs": {"library|input_1": {"src": "hda", "id": "983882a617d10737"}, "library|type": "single"}, "job": {"model_class": "Job", "id": "44d4d8d711419aa2", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:15:15.341139", "update_time": "2024-09-23T07:15:29.202866", "galaxy_version": "24.1", "external_id": "gxy-c69gb", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/4/2/dataset_54241817-d0f8-4bf7-aea5-98c252f03835.dat' 'simple_fasta_gz.fa.gz' && cutadapt -j=${GALAXY_SLOTS:-4} --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fa.gz' 'simple_fasta_gz.fa.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 240, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "983882a617d10737", "src": "hda", "uuid": "54241817-d0f8-4bf7-aea5-98c252f03835"}}, "outputs": {"out1": {"id": "3c89601b05e37c90", "src": "hda", "uuid": "2ffc1b46-32a0-4d25-82c6-e10a00a7fe9d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fa.gz simple_fasta_gz.fa.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.086 s (43177.485 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 18 bp\nTotal written (filtered): 18 bp (100.0%)\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fa.gz simple_fasta_gz.fa.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.086 s (43177.485 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 18 bp\nTotal written (filtered): 18 bp (100.0%)\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:15:17", "plugin": "core", "name": "end_epoch", "raw_value": "1727075717.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:15:16", "plugin": "core", "name": "start_epoch", "raw_value": "1727075716.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-42", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 42, "time_seconds": 32.29194927215576, "inputs": {"library|input_1": {"src": "hda", "id": "ef33e62ed7cc0470"}, "library|r1|adapters_0|adapter_source|adapter": "XXXXXX", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|quality_cutoff": "10", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "3de64f972679a4bf", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:51:55.452521", "update_time": "2024-09-23T06:52:08.193605", "galaxy_version": "24.1", "external_id": "gxy-plg2b", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/6/2/0/dataset_62059f5a-d719-49c2-bb57-6af4dda9e481.dat' 'illumina64_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'XXXXXX' --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o 'out1.fq' 'illumina64_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"10\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 119, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"XXXXXX\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "ef33e62ed7cc0470", "src": "hda", "uuid": "62059f5a-d719-49c2-bb57-6af4dda9e481"}}, "outputs": {"out1": {"id": "dcf528637d220b91", "src": "hda", "uuid": "6b94ffd3-79cd-4fdd-bd5e-a7f5f817794a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a XXXXXX --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o out1.fq illumina64_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (2095.032 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 20\nReads with adapters: 0 (0.0%)\nReads written (passing filters): 20 (100.0%)\n\nTotal basepairs processed: 1,900 bp\nQuality-trimmed: 1,021 bp (53.7%)\nTotal written (filtered): 879 bp (46.3%)\n\n=== Adapter 1 ===\n\nSequence: XXXXXX; Type: regular 3'; Length: 6; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a XXXXXX --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o out1.fq illumina64_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.042 s (2095.032 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 20\nReads with adapters: 0 (0.0%)\nReads written (passing filters): 20 (100.0%)\n\nTotal basepairs processed: 1,900 bp\nQuality-trimmed: 1,021 bp (53.7%)\nTotal written (filtered): 879 bp (46.3%)\n\n=== Adapter 1 ===\n\nSequence: XXXXXX; Type: regular 3'; Length: 6; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:51:57", "plugin": "core", "name": "end_epoch", "raw_value": "1727074317.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:51:56", "plugin": "core", "name": "start_epoch", "raw_value": "1727074316.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-42", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 42, "time_seconds": 33.63849329948425, "inputs": {"library|input_1": {"src": "hda", "id": "5c8f33675f7c28a2"}, "library|r1|adapters_0|adapter_source|adapter": "XXXXXX", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|quality_cutoff": "10", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "257aab356ba474f6", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:15:49.475862", "update_time": "2024-09-23T07:16:02.719994", "galaxy_version": "24.1", "external_id": "gxy-52h6r", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/4/8/c/dataset_48c24b95-05e6-4f49-87f6-449cc996b545.dat' 'illumina64_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'XXXXXX' --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o 'out1.fq' 'illumina64_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"10\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 242, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"XXXXXX\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "5c8f33675f7c28a2", "src": "hda", "uuid": "48c24b95-05e6-4f49-87f6-449cc996b545"}}, "outputs": {"out1": {"id": "7283e8040bdfa16c", "src": "hda", "uuid": "bd36a7dd-4c5b-44af-9079-4710ecda0921"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a XXXXXX --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o out1.fq illumina64_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (2025.628 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 20\nReads with adapters: 0 (0.0%)\nReads written (passing filters): 20 (100.0%)\n\nTotal basepairs processed: 1,900 bp\nQuality-trimmed: 1,021 bp (53.7%)\nTotal written (filtered): 879 bp (46.3%)\n\n=== Adapter 1 ===\n\nSequence: XXXXXX; Type: regular 3'; Length: 6; Trimmed: 0 times\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a XXXXXX --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o out1.fq illumina64_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (2025.628 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 20\nReads with adapters: 0 (0.0%)\nReads written (passing filters): 20 (100.0%)\n\nTotal basepairs processed: 1,900 bp\nQuality-trimmed: 1,021 bp (53.7%)\nTotal written (filtered): 879 bp (46.3%)\n\n=== Adapter 1 ===\n\nSequence: XXXXXX; Type: regular 3'; Length: 6; Trimmed: 0 times\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:15:51", "plugin": "core", "name": "end_epoch", "raw_value": "1727075751.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:15:50", "plugin": "core", "name": "start_epoch", "raw_value": "1727075750.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-43", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 43, "time_seconds": 32.29862713813782, "inputs": {"library|input_1": {"src": "hda", "id": "5daeb9b5515423e9"}, "library|type": "single", "other_trimming_options|quality_cutoff": "10", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "7eb981d2085bfd9e", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:52:27.490264", "update_time": "2024-09-23T06:52:40.397786", "galaxy_version": "24.1", "external_id": "gxy-ghxtc", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/a/f/b/dataset_afbaa70e-4905-4642-8767-b0391a81b71f.dat' 'illumina64_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o 'out1.fq' 'illumina64_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"10\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 121, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "5daeb9b5515423e9", "src": "hda", "uuid": "afbaa70e-4905-4642-8767-b0391a81b71f"}}, "outputs": {"out1": {"id": "44467cb263d7ddf2", "src": "hda", "uuid": "f998029d-fec0-449e-82b8-3d5f3d96bba9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o out1.fq illumina64_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.032 s (1605.427 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 20\nReads written (passing filters): 20 (100.0%)\n\nTotal basepairs processed: 1,900 bp\nQuality-trimmed: 1,021 bp (53.7%)\nTotal written (filtered): 879 bp (46.3%)\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o out1.fq illumina64_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.032 s (1605.427 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 20\nReads written (passing filters): 20 (100.0%)\n\nTotal basepairs processed: 1,900 bp\nQuality-trimmed: 1,021 bp (53.7%)\nTotal written (filtered): 879 bp (46.3%)\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:52:30", "plugin": "core", "name": "end_epoch", "raw_value": "1727074350.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:52:29", "plugin": "core", "name": "start_epoch", "raw_value": "1727074349.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-43", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 43, "time_seconds": 34.80425024032593, "inputs": {"library|input_1": {"src": "hda", "id": "df4da4e0e70a7cba"}, "library|type": "single", "other_trimming_options|quality_cutoff": "10", "filter_options|minimum_length": "0"}, "job": {"model_class": "Job", "id": "ac76b55aa7119dde", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:16:23.286905", "update_time": "2024-09-23T07:16:37.873729", "galaxy_version": "24.1", "external_id": "gxy-pz4bh", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/9/f/6/dataset_9f6a2f43-819c-4e2e-9796-b39500eba1c0.dat' 'illumina64_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o 'out1.fq' 'illumina64_fastq.fq'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"10\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 244, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "df4da4e0e70a7cba", "src": "hda", "uuid": "9f6a2f43-819c-4e2e-9796-b39500eba1c0"}}, "outputs": {"out1": {"id": "9793c3ab30596a97", "src": "hda", "uuid": "a5bd74c9-d888-44b9-9dcb-6b18bdcd1a3e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o out1.fq illumina64_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.034 s (1707.113 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 20\nReads written (passing filters): 20 (100.0%)\n\nTotal basepairs processed: 1,900 bp\nQuality-trimmed: 1,021 bp (53.7%)\nTotal written (filtered): 879 bp (46.3%)\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=10 --quality-base=64 -o out1.fq illumina64_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.034 s (1707.113 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 20\nReads written (passing filters): 20 (100.0%)\n\nTotal basepairs processed: 1,900 bp\nQuality-trimmed: 1,021 bp (53.7%)\nTotal written (filtered): 879 bp (46.3%)\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:16:26", "plugin": "core", "name": "end_epoch", "raw_value": "1727075786.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:16:25", "plugin": "core", "name": "start_epoch", "raw_value": "1727075785.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-44", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 44, "time_seconds": 33.11443305015564, "inputs": {"library|input_1": {"src": "hda", "id": "822adea1c0031a18"}, "library|type": "single", 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"\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": "[\"report\", \"info_file\"]", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"0.9\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 123, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "822adea1c0031a18", "src": "hda", "uuid": "361d24f5-8bfc-4fb1-b55e-215a173e561e"}}, "outputs": {"out1": {"id": "7e9793e09e73a63c", "src": "hda", "uuid": "3665daa4-95c3-48c4-876a-5a7ebd6c9bc7"}, "report": {"id": "197335a38b6e37dd", "src": "hda", "uuid": "bce9e1d0-ab51-4b58-9106-8a222612daed"}, "info_file": {"id": "4cf10b4ccb2e9ad8", "src": "hda", "uuid": "9adcd953-2023-492f-a7bb-ab01dd45809b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], 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"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": "[\"report\", \"info_file\"]", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"0.9\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"0\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 246, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "342dfa457583c217", "src": "hda", "uuid": "7cb1e1a7-646d-445c-9974-68c5fee67f38"}}, "outputs": {"out1": {"id": "b202d6941b3eabf3", "src": "hda", "uuid": "f3598316-86de-4af0-9059-bbef28391a22"}, "report": {"id": "c749b0c2299daa9f", "src": "hda", "uuid": "4a453ac7-6270-44c6-9378-11ee0c8d19c8"}, "info_file": {"id": "f95322f79f3dec14", "src": "hda", "uuid": "e03319bb-717b-45e8-aab3-ca5a159e79cb"}}, "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": "2024-09-23 07:17:00", "plugin": "core", "name": "end_epoch", "raw_value": "1727075820.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:16:59", "plugin": "core", "name": "start_epoch", "raw_value": "1727075819.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-45", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 45, "time_seconds": 32.43673396110535, "inputs": {"library|input_1": {"src": "hda", "id": "99d050715248c657"}, "library|r1|anywhere_adapters_0|adapter_source|adapter": "ACGTACGT", "library|r1|anywhere_adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|match_read_wildcards": true}, "job": {"model_class": "Job", "id": "50eab474c7f1170d", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:53:33.156706", "update_time": "2024-09-23T06:53:46.000232", "galaxy_version": "24.1", "external_id": "gxy-xjmkr", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/c/7/dataset_5c7a7669-e818-4d91-9987-5a18d9b7c3f4.dat' 'wildcard_fa.fa' && cutadapt -j=${GALAXY_SLOTS:-4} -b 'ACGTACGT' --error-rate=0.1 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o 'out1.fa' 'wildcard_fa.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": true, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"ACGTACGT\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "99d050715248c657", "src": "hda", "uuid": "5c7a7669-e818-4d91-9987-5a18d9b7c3f4"}}, "outputs": {"out1": {"id": "06ad6eb972ef127c", "src": "hda", "uuid": "438c15fc-063b-4132-a875-68febfe5d873"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -b ACGTACGT --error-rate=0.1 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o out1.fa wildcard_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (20326.734 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 2 (100.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 32 bp\nTotal written (filtered): 16 bp (50.0%)\n\n=== Adapter 1 ===\n\nSequence: ACGTACGT; Type: variable 5'/3'; Length: 8; Trimmed: 2 times\n2 times, it overlapped the 5' end of a read\n0 times, it overlapped the 3' end or was within the read\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-8 bp: 0\n\nOverview of removed sequences (5')\nlength\tcount\texpect\tmax.err\terror counts\n8\t2\t0.0\t0\t2\n\n\n\nOverview of removed sequences (3' or within)\nlength\tcount\texpect\tmax.err\terror counts\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -b ACGTACGT --error-rate=0.1 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o out1.fa wildcard_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (20326.734 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 2 (100.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 32 bp\nTotal written (filtered): 16 bp (50.0%)\n\n=== Adapter 1 ===\n\nSequence: ACGTACGT; Type: variable 5'/3'; Length: 8; Trimmed: 2 times\n2 times, it overlapped the 5' end of a read\n0 times, it overlapped the 3' end or was within the read\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-8 bp: 0\n\nOverview of removed sequences (5')\nlength\tcount\texpect\tmax.err\terror counts\n8\t2\t0.0\t0\t2\n\n\n\nOverview of removed sequences (3' or within)\nlength\tcount\texpect\tmax.err\terror counts\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:53:35", "plugin": "core", "name": "end_epoch", "raw_value": "1727074415.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:53:34", "plugin": "core", "name": "start_epoch", "raw_value": "1727074414.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-45", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 45, "time_seconds": 34.45895457267761, "inputs": {"library|input_1": {"src": "hda", "id": "8796d6bd65a7047a"}, "library|r1|anywhere_adapters_0|adapter_source|adapter": "ACGTACGT", "library|r1|anywhere_adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|match_read_wildcards": true}, "job": {"model_class": "Job", "id": "fdd73cfc0129b814", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:17:32.802516", "update_time": "2024-09-23T07:17:46.490910", "galaxy_version": "24.1", "external_id": "gxy-4jtcc", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/f/b/2/dataset_fb270e97-5c98-47aa-815d-9d100dcfb252.dat' 'wildcard_fa.fa' && cutadapt -j=${GALAXY_SLOTS:-4} -b 'ACGTACGT' --error-rate=0.1 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o 'out1.fa' 'wildcard_fa.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": true, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 250, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"ACGTACGT\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "8796d6bd65a7047a", "src": "hda", "uuid": "fb270e97-5c98-47aa-815d-9d100dcfb252"}}, "outputs": {"out1": {"id": "89781d424ba22224", "src": "hda", "uuid": "95f2c60a-6a18-441b-a5ce-1ed3d307699a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -b ACGTACGT --error-rate=0.1 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o out1.fa wildcard_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.044 s (21990.657 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 2 (100.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 32 bp\nTotal written (filtered): 16 bp (50.0%)\n\n=== Adapter 1 ===\n\nSequence: ACGTACGT; Type: variable 5'/3'; Length: 8; Trimmed: 2 times\n2 times, it overlapped the 5' end of a read\n0 times, it overlapped the 3' end or was within the read\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-8 bp: 0\n\nOverview of removed sequences (5')\nlength\tcount\texpect\tmax.err\terror counts\n8\t2\t0.0\t0\t2\n\n\n\nOverview of removed sequences (3' or within)\nlength\tcount\texpect\tmax.err\terror counts\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -b ACGTACGT --error-rate=0.1 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o out1.fa wildcard_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.044 s (21990.657 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 2 (100.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 32 bp\nTotal written (filtered): 16 bp (50.0%)\n\n=== Adapter 1 ===\n\nSequence: ACGTACGT; Type: variable 5'/3'; Length: 8; Trimmed: 2 times\n2 times, it overlapped the 5' end of a read\n0 times, it overlapped the 3' end or was within the read\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-8 bp: 0\n\nOverview of removed sequences (5')\nlength\tcount\texpect\tmax.err\terror counts\n8\t2\t0.0\t0\t2\n\n\n\nOverview of removed sequences (3' or within)\nlength\tcount\texpect\tmax.err\terror counts\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:17:35", "plugin": "core", "name": "end_epoch", "raw_value": "1727075855.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:17:34", "plugin": "core", "name": "start_epoch", "raw_value": "1727075854.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-46", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 46, "time_seconds": 33.02557349205017, "inputs": {"library|input_1": {"src": "hda", "id": "e94a60275527f452"}, "library|r1|adapters_0|adapter_source|adapter": "GGGGGGG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|error_rate": "0", "adapter_options|match_read_wildcards": true}, "job": {"model_class": "Job", "id": "98041e0b7758fa35", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:54:06.232408", "update_time": "2024-09-23T06:54:19.408601", "galaxy_version": "24.1", "external_id": "gxy-kb4cl", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/e/9/8/dataset_e983159b-ed3f-4692-8ceb-c47e7533eb8b.dat' 'wildcardN_fa.fa' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'GGGGGGG' --error-rate=0.0 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o 'out1.fa' 'wildcardN_fa.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.0\", \"match_read_wildcards\": true, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 129, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"GGGGGGG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "e94a60275527f452", "src": "hda", "uuid": "e983159b-ed3f-4692-8ceb-c47e7533eb8b"}}, "outputs": {"out1": {"id": "1ab195e8b38743af", "src": "hda", "uuid": "97e67e3a-5450-41ad-a355-daa166d9d3e1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a GGGGGGG --error-rate=0.0 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o out1.fa wildcardN_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.044 s (14774.084 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 2 (66.7%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 30 bp\nTotal written (filtered): 16 bp (53.3%)\n\n=== Adapter 1 ===\n\nSequence: GGGGGGG; Type: regular 3'; Length: 7; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-7 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n7\t2\t0.0\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a GGGGGGG --error-rate=0.0 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o out1.fa wildcardN_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.044 s (14774.084 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 2 (66.7%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 30 bp\nTotal written (filtered): 16 bp (53.3%)\n\n=== Adapter 1 ===\n\nSequence: GGGGGGG; Type: regular 3'; Length: 7; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-7 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n7\t2\t0.0\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:54:08", "plugin": "core", "name": "end_epoch", "raw_value": "1727074448.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:54:07", "plugin": "core", "name": "start_epoch", "raw_value": "1727074447.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-46", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 46, "time_seconds": 35.474759578704834, "inputs": {"library|input_1": {"src": "hda", "id": "38568f59e23ee481"}, "library|r1|adapters_0|adapter_source|adapter": "GGGGGGG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "adapter_options|error_rate": "0", "adapter_options|match_read_wildcards": true}, "job": {"model_class": "Job", "id": "77d432dca06c69ef", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:18:06.955444", "update_time": "2024-09-23T07:18:21.998390", "galaxy_version": "24.1", "external_id": "gxy-fzwvl", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/c/1/d/dataset_c1d8c9cf-dc34-45b3-aca8-0b44db6e4471.dat' 'wildcardN_fa.fa' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'GGGGGGG' --error-rate=0.0 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o 'out1.fa' 'wildcardN_fa.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.0\", \"match_read_wildcards\": true, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 252, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"GGGGGGG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "38568f59e23ee481", "src": "hda", "uuid": "c1d8c9cf-dc34-45b3-aca8-0b44db6e4471"}}, "outputs": {"out1": {"id": "4254a171d8e0a67a", "src": "hda", "uuid": "032bf56b-8748-461f-b5ae-719097c48e5b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a GGGGGGG --error-rate=0.0 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o out1.fa wildcardN_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14345.646 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 2 (66.7%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 30 bp\nTotal written (filtered): 16 bp (53.3%)\n\n=== Adapter 1 ===\n\nSequence: GGGGGGG; Type: regular 3'; Length: 7; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-7 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n7\t2\t0.0\t0\t2\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a GGGGGGG --error-rate=0.0 --times=1 --overlap=3 --match-read-wildcards --action=trim --minimum-length=1 -o out1.fa wildcardN_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.043 s (14345.646 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 2 (66.7%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 3 (100.0%)\n\nTotal basepairs processed: 30 bp\nTotal written (filtered): 16 bp (53.3%)\n\n=== Adapter 1 ===\n\nSequence: GGGGGGG; Type: regular 3'; Length: 7; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-7 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n7\t2\t0.0\t0\t2\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:18:10", "plugin": "core", "name": "end_epoch", "raw_value": "1727075890.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:18:09", "plugin": "core", "name": "start_epoch", "raw_value": "1727075889.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-47", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 47, "time_seconds": 10.556138515472412, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "cutadapt/4.9+galaxy1-47", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 47, "time_seconds": 33.82771348953247, "inputs": {"library|input_1": {"src": "hda", "id": "c4884b7ca97dac41"}, "library|input_2": {"src": "hda", "id": "e163c494cd39d3a3"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|type": "paired"}, "job": {"model_class": "Job", "id": "fec5d94b97744176", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "error", "exit_code": 1, "create_time": "2024-09-23T07:18:43.273538", "update_time": "2024-09-23T07:18:56.488190", "galaxy_version": "24.1", "external_id": "gxy-snjfb", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/6/b/2/dataset_6b23f6b9-3de3-4e6f-94b1-d977648ed349.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/6/9/f/dataset_69ff2f45-a382-4181-a720-19f348b1eebd.dat' 'bwa-mem-fastq_mispaired2_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz' 'bwa-mem-fastq_mispaired2_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 254, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 255, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "c4884b7ca97dac41", "src": "hda", "uuid": "6b23f6b9-3de3-4e6f-94b1-d977648ed349"}, "library|input_2": {"id": "e163c494cd39d3a3", "src": "hda", "uuid": "69ff2f45-a382-4181-a720-19f348b1eebd"}}, "outputs": {"out1": {"id": "933f5b704cc607b0", "src": "hda", "uuid": "859fc391-6fe9-4d36-abc7-74356823ce10"}, "out2": {"id": "c1f040d4177fdc64", "src": "hda", "uuid": "6ead2641-954c-4b84-9264-0e3b41e8da7b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq_mispaired2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\n", "tool_stderr": "Error in sequence file at unknown line: Reads are improperly paired. Read name 'M01368:8:000000000-A3GHV:1:1101:6911:8255/1' in file 1 does not match 'M01368:8:000000000-A3GHV:1:1101:14518:9998/2' in file 2.\n", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq_mispaired2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\n", "stderr": "Error in sequence file at unknown line: Reads are improperly paired. Read name 'M01368:8:000000000-A3GHV:1:1101:6911:8255/1' in file 1 does not match 'M01368:8:000000000-A3GHV:1:1101:14518:9998/2' in file 2.\n", "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-23 07:18:45", "plugin": "core", "name": "end_epoch", "raw_value": "1727075925.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:18:45", "plugin": "core", "name": "start_epoch", "raw_value": "1727075925.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-5", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 5, "time_seconds": 10.84730339050293, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "cutadapt/4.9+galaxy1-5", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 5, "time_seconds": 24.77695894241333, "inputs": {"library|input_1": {"src": "hda", "id": "1c94a0697c8cb3cc"}, "library|r1|adapters_0|adapter_source|adapter": "TTAGACATATCTCCGTCG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "filter_options|discard_trimmed": true}, "job": {"model_class": "Job", "id": "ef33e62ed7cc0470", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-09-23T06:57:04.117047", "update_time": "2024-09-23T06:57:09.697897", "galaxy_version": "24.1", "external_id": "gxy-cz2cb", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/6/6/5/dataset_665f5959-d978-43b5-88f6-d15616b4d500.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'TTAGACATATCTCCGTCG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-trimmed --minimum-length=1 -o 'out1.fq' 'cutadapt_small_fastq.fq'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": true, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 145, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"TTAGACATATCTCCGTCG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "1c94a0697c8cb3cc", "src": "hda", "uuid": "665f5959-d978-43b5-88f6-d15616b4d500"}}, "outputs": {"out1": {"id": "5772f72a02a89bf1", "src": "hda", "uuid": "f5b30055-4f49-4586-ae0a-07ac51200bec"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a TTAGACATATCTCCGTCG --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-trimmed --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (13716.936 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 2 (66.7%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 1 (33.3%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 34 bp (33.3%)\n\n=== Adapter 1 ===\n\nSequence: TTAGACATATCTCCGTCG; Type: regular 3'; Length: 18; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-18 bp: 1\n\nBases preceding removed adapters:\n A: 50.0%\n C: 50.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n10\t1\t0.0\t1\t0 1\n12\t1\t0.0\t1\t0 1\n", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a TTAGACATATCTCCGTCG --error-rate=0.1 --times=1 --overlap=3 --action=trim --discard-trimmed --minimum-length=1 -o out1.fq cutadapt_small_fastq.fq\nProcessing single-end reads on 5 cores ...\nFinished in 0.041 s (13716.936 \u00b5s/read; 0.00 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 3\nReads with adapters: 2 (66.7%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 1 (33.3%)\n\nTotal basepairs processed: 102 bp\nTotal written (filtered): 34 bp (33.3%)\n\n=== Adapter 1 ===\n\nSequence: TTAGACATATCTCCGTCG; Type: regular 3'; Length: 18; Trimmed: 2 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-18 bp: 1\n\nBases preceding removed adapters:\n A: 50.0%\n C: 50.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n10\t1\t0.0\t1\t0 1\n12\t1\t0.0\t1\t0 1\n", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "cutadapt/4.9+galaxy1-6", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 6, "time_seconds": 35.61858034133911, "inputs": {"library|input_1": {"src": "hda", "id": "b2b30bea50c85ec5"}, "library|input_2": {"src": "hda", "id": "1232924e6a047ad5"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|pair_adapters": true, "library|type": "paired"}, "job": {"model_class": "Job", "id": "b2b30bea50c85ec5", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:32:15.325709", "update_time": "2024-09-23T06:32:30.022559", "galaxy_version": "24.1", "external_id": "gxy-r9z9z", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/8/4/3/dataset_843b64ae-1029-412d-96b9-70747c354c05.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/4/f/1/dataset_4f1f7b0d-b742-432a-adab-2810def27598.dat' 'bwa-mem-fastq2_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --pair-adapters --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz' 'bwa-mem-fastq2_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 18, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 19, \"src\": \"hda\"}]}, \"pair_adapters\": true, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "output_selector": null, "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"library|input_1": {"id": "b2b30bea50c85ec5", "src": "hda", "uuid": "843b64ae-1029-412d-96b9-70747c354c05"}, "library|input_2": {"id": "1232924e6a047ad5", "src": "hda", "uuid": "4f1f7b0d-b742-432a-adab-2810def27598"}}, "outputs": {"out1": {"id": "052b6112ed53a88e", "src": "hda", "uuid": "73541cde-0753-41a8-b977-4ccfaac2e2d9"}, "out2": {"id": "06680d0fd17de9f3", "src": "hda", "uuid": "2fb9b284-b516-414f-80b8-1c5a48ee1caf"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --pair-adapters --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.175 s (1764.175 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 1 (1.0%)\n Read 2 with adapter: 1 (1.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,692 bp (100.0%)\n Read 1: 24,846 bp\n Read 2: 24,846 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t1\t1.5\t0\t1\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t1\t1.5\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --pair-adapters --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.175 s (1764.175 \u00b5s/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 1 (1.0%)\n Read 2 with adapter: 1 (1.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,692 bp (100.0%)\n Read 1: 24,846 bp\n Read 2: 24,846 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t1\t1.5\t0\t1\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t1\t1.5\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:32:17", "plugin": "core", "name": "start_epoch", "raw_value": "1727073137.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:32:18", "plugin": "core", "name": "end_epoch", "raw_value": "1727073138.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-6", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 6, "time_seconds": 34.28704214096069, "inputs": {"library|input_1": {"src": "hda", "id": "ff0dd2107873f620"}, "library|input_2": {"src": "hda", "id": "df03dc4dc71cf3b3"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|r2|adapters2_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r2|adapters2_0|adapter_source|adapter_source_list": "user", "library|pair_adapters": true, "library|type": "paired"}, "job": {"model_class": "Job", "id": "44467cb263d7ddf2", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:57:30.029296", "update_time": "2024-09-23T06:57:43.564100", "galaxy_version": "24.1", "external_id": "gxy-gdztt", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/9/6/4/dataset_96473a62-a4e7-4a57-93ca-c4fdde66a7f3.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/5/6/7/dataset_5673bad0-e1aa-4985-8706-d28d7c71ddcd.dat' 'bwa-mem-fastq2_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --pair-adapters --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz' 'bwa-mem-fastq2_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 147, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 148, \"src\": \"hda\"}]}, \"pair_adapters\": true, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}"}, "inputs": {"library|input_1": {"id": "ff0dd2107873f620", "src": "hda", "uuid": "96473a62-a4e7-4a57-93ca-c4fdde66a7f3"}, "library|input_2": {"id": "df03dc4dc71cf3b3", "src": "hda", "uuid": "5673bad0-e1aa-4985-8706-d28d7c71ddcd"}}, "outputs": {"out1": {"id": "fe50ce8fea59090d", "src": "hda", "uuid": "c0b6f863-1fc2-460c-b8f5-b709281237dc"}, "out2": {"id": "72d521314af318d4", "src": "hda", "uuid": "4de47c63-e4bd-4dc0-b230-61fa64fc14bc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --pair-adapters --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.168 s (1693.061 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 1 (1.0%)\n Read 2 with adapter: 1 (1.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,692 bp (100.0%)\n Read 1: 24,846 bp\n Read 2: 24,846 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t1\t1.5\t0\t1\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t1\t1.5\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --pair-adapters --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\nFinished in 0.168 s (1693.061 \u00b5s/read; 0.04 M reads/minute).\n\n=== Summary ===\n\nTotal read pairs processed: 99\n Read 1 with adapter: 1 (1.0%)\n Read 2 with adapter: 1 (1.0%)\n\n== Read fate breakdown ==\nPairs that were too short: 0 (0.0%)\nPairs written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 49,698 bp\n Read 1: 24,849 bp\n Read 2: 24,849 bp\nTotal written (filtered): 49,692 bp (100.0%)\n Read 1: 24,846 bp\n Read 2: 24,846 bp\n\n=== First read: Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t1\t1.5\t0\t1\n\n\n=== Second read: Adapter 2 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 0.0%\n T: 100.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t1\t1.5\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:57:32", "plugin": "core", "name": "end_epoch", "raw_value": "1727074652.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:57:31", "plugin": "core", "name": "start_epoch", "raw_value": "1727074651.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-7", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 7, "time_seconds": 36.051870822906494, "inputs": {"library|input_1": {"src": "hda", "id": "3c96dc82e0e57c39"}, "library|r1|adapters_0|adapter_source|adapter": "AAAGATG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "output_selector": ["rest_file", "json_stats"]}, "job": {"model_class": "Job", "id": "052b6112ed53a88e", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:32:51.310576", "update_time": "2024-09-23T06:33:05.968987", "galaxy_version": "24.1", "external_id": "gxy-cjkgl", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/3/8/4/dataset_3844ee54-5d8f-4778-8c8b-d6d3d0573fb7.dat' 'cutadapt_rest_fa.fa' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AAAGATG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --json=stats.json -r='rest_output.fa' -o 'out1.fa' 'cutadapt_rest_fa.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 22, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AAAGATG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "output_selector": "[\"rest_file\", \"json_stats\"]", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"library|input_1": {"id": "3c96dc82e0e57c39", "src": "hda", "uuid": "3844ee54-5d8f-4778-8c8b-d6d3d0573fb7"}}, "outputs": {"out1": {"id": "d4266afed72fbe9d", "src": "hda", "uuid": "77ad256c-bf1a-454d-9c1b-ad61818a8f81"}, "rest_output": {"id": "d34d62e91a86c784", "src": "hda", "uuid": "bbd83bc1-7280-486f-94f1-850ef7796da7"}, "json_stats": {"id": "f35c11b8830d577c", "src": "hda", "uuid": "9285a7fc-da6a-4d83-9a9c-0de99c437f50"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AAAGATG --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --json=stats.json -r=rest_output.fa -o out1.fa cutadapt_rest_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.050 s (10013.866 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 5\nReads with adapters: 5 (100.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 5 (100.0%)\n\nTotal basepairs processed: 97 bp\nTotal written (filtered): 35 bp (36.1%)\n\n=== Adapter 1 ===\n\nSequence: AAAGATG; Type: regular 3'; Length: 7; Trimmed: 5 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-7 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 100.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n7\t1\t0.0\t0\t1\n12\t1\t0.0\t0\t1\n14\t2\t0.0\t0\t2\n15\t1\t0.0\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AAAGATG --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --json=stats.json -r=rest_output.fa -o out1.fa cutadapt_rest_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.050 s (10013.866 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 5\nReads with adapters: 5 (100.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 5 (100.0%)\n\nTotal basepairs processed: 97 bp\nTotal written (filtered): 35 bp (36.1%)\n\n=== Adapter 1 ===\n\nSequence: AAAGATG; Type: regular 3'; Length: 7; Trimmed: 5 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-7 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 100.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n7\t1\t0.0\t0\t1\n12\t1\t0.0\t0\t1\n14\t2\t0.0\t0\t2\n15\t1\t0.0\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:32:53", "plugin": "core", "name": "start_epoch", "raw_value": "1727073173.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:32:54", "plugin": "core", "name": "end_epoch", "raw_value": "1727073174.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-7", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 7, "time_seconds": 32.8341326713562, "inputs": {"library|input_1": {"src": "hda", "id": "e3f5a8c3be19492f"}, "library|r1|adapters_0|adapter_source|adapter": "AAAGATG", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "output_selector": ["rest_file", "json_stats"]}, "job": {"model_class": "Job", "id": "7e9793e09e73a63c", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:58:02.881304", "update_time": "2024-09-23T06:58:16.031517", "galaxy_version": "24.1", "external_id": "gxy-gf4kp", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/4/e/e/dataset_4ee5cd78-08db-42e1-a52c-3a860c27330c.dat' 'cutadapt_rest_fa.fa' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AAAGATG' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --json=stats.json -r='rest_output.fa' -o 'out1.fa' 'cutadapt_rest_fa.fa'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": "[\"rest_file\", \"json_stats\"]", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 151, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AAAGATG\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "e3f5a8c3be19492f", "src": "hda", "uuid": "4ee5cd78-08db-42e1-a52c-3a860c27330c"}}, "outputs": {"out1": {"id": "accfa32b480a4bc2", "src": "hda", "uuid": "562b859f-a4c3-4a1b-bc95-cf23a9b3e885"}, "rest_output": {"id": "880f77f39a3c619b", "src": "hda", "uuid": "425a971b-5f10-42e0-a15c-2031fb1eca57"}, "json_stats": {"id": "45dd93d5d0c726a3", "src": "hda", "uuid": "2b8cab80-d3e4-4a86-bb4d-f331b7435783"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AAAGATG --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --json=stats.json -r=rest_output.fa -o out1.fa cutadapt_rest_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.045 s (9003.210 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 5\nReads with adapters: 5 (100.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 5 (100.0%)\n\nTotal basepairs processed: 97 bp\nTotal written (filtered): 35 bp (36.1%)\n\n=== Adapter 1 ===\n\nSequence: AAAGATG; Type: regular 3'; Length: 7; Trimmed: 5 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-7 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 100.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n7\t1\t0.0\t0\t1\n12\t1\t0.0\t0\t1\n14\t2\t0.0\t0\t2\n15\t1\t0.0\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AAAGATG --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --json=stats.json -r=rest_output.fa -o out1.fa cutadapt_rest_fa.fa\nProcessing single-end reads on 5 cores ...\nFinished in 0.045 s (9003.210 \u00b5s/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 5\nReads with adapters: 5 (100.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 5 (100.0%)\n\nTotal basepairs processed: 97 bp\nTotal written (filtered): 35 bp (36.1%)\n\n=== Adapter 1 ===\n\nSequence: AAAGATG; Type: regular 3'; Length: 7; Trimmed: 5 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-7 bp: 0\n\nBases preceding removed adapters:\n A: 0.0%\n C: 0.0%\n G: 100.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n7\t1\t0.0\t0\t1\n12\t1\t0.0\t0\t1\n14\t2\t0.0\t0\t2\n15\t1\t0.0\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:58:05", "plugin": "core", "name": "end_epoch", "raw_value": "1727074685.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:58:04", "plugin": "core", "name": "start_epoch", "raw_value": "1727074684.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-8", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 8, "time_seconds": 35.561736822128296, "inputs": {"library|input_1": {"src": "hda", "id": "94946436656c3f78"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|nextseq_trim": "20"}, "job": {"model_class": "Job", "id": "3c96dc82e0e57c39", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:33:27.078323", "update_time": "2024-09-23T06:33:42.332850", "galaxy_version": "24.1", "external_id": "gxy-zf4gl", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/0/a/d/dataset_0ada8cc8-8f55-4c5c-8266-a093e44acf73.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 --minimum-length=1 -o 'out1.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 26, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"20\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "output_selector": null, "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"library|input_1": {"id": "94946436656c3f78", "src": "hda", "uuid": "0ada8cc8-8f55-4c5c-8266-a093e44acf73"}}, "outputs": {"out1": {"id": "5ec37b3ed164ec90", "src": "hda", "uuid": "7a3fe086-eb3c-4d34-a105-e68af331c09b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 --minimum-length=1 -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.094 s (946.844 \u00b5s/read; 0.06 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 4 (4.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 286 bp (1.2%)\nTotal written (filtered): 24,550 bp (98.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 75.0%\n G: 25.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t3\t1.5\t0\t3\n4\t1\t0.4\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 --minimum-length=1 -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.094 s (946.844 \u00b5s/read; 0.06 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 4 (4.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 286 bp (1.2%)\nTotal written (filtered): 24,550 bp (98.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 75.0%\n G: 25.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t3\t1.5\t0\t3\n4\t1\t0.4\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:33:29", "plugin": "core", "name": "start_epoch", "raw_value": "1727073209.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:33:30", "plugin": "core", "name": "end_epoch", "raw_value": "1727073210.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-8", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 8, "time_seconds": 32.32243728637695, "inputs": {"library|input_1": {"src": "hda", "id": "b46b3e897455561b"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "other_trimming_options|nextseq_trim": "20"}, "job": {"model_class": "Job", "id": "4cf10b4ccb2e9ad8", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:58:36.223232", "update_time": "2024-09-23T06:58:49.176675", "galaxy_version": "24.1", "external_id": "gxy-57tc2", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/6/8/d/dataset_68d2bfd8-c390-4d3d-a68d-754d47e431dd.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 --minimum-length=1 -o 'out1.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz'", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": null, "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"20\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 155, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "b46b3e897455561b", "src": "hda", "uuid": "68d2bfd8-c390-4d3d-a68d-754d47e431dd"}}, "outputs": {"out1": {"id": "747972a3e3c020d0", "src": "hda", "uuid": "aa9fde45-09f4-496a-a8f1-7879b5eacdc1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 --minimum-length=1 -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.099 s (1004.489 \u00b5s/read; 0.06 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 4 (4.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 286 bp (1.2%)\nTotal written (filtered): 24,550 bp (98.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 75.0%\n G: 25.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t3\t1.5\t0\t3\n4\t1\t0.4\t0\t1\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "This is cutadapt 4.9 with Python 3.12.5\nCommand line parameters: -j=5 -a AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 --minimum-length=1 -o out1.fq.gz bwa-mem-fastq1_fq_gz.fq.gz\nProcessing single-end reads on 5 cores ...\nFinished in 0.099 s (1004.489 \u00b5s/read; 0.06 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 4 (4.0%)\n\n== Read fate breakdown ==\nReads that were too short: 0 (0.0%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 286 bp (1.2%)\nTotal written (filtered): 24,550 bp (98.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times\n\nMinimum overlap: 3\nNo. of allowed errors:\n1-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 75.0%\n G: 25.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n3\t3\t1.5\t0\t3\n4\t1\t0.4\t0\t1\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:58:38", "plugin": "core", "name": "end_epoch", "raw_value": "1727074718.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:58:37", "plugin": "core", "name": "start_epoch", "raw_value": "1727074717.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "cutadapt/4.9+galaxy1-9", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 9, "time_seconds": 24.458197832107544, "inputs": {"library|input_1": {"src": "hda", "id": "a6dc655213a10cb8"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "output_selector": ["report", "info_file"]}, "job": {"model_class": "Job", "id": "d34d62e91a86c784", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-09-23T06:34:02.635518", "update_time": "2024-09-23T06:34:07.056899", "galaxy_version": "24.1", "external_id": "gxy-rbhsm", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/7/b/dataset_57b443b6-2449-4c1e-940d-705244af818a.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --info-file='/galaxy/server/database/objects/3/8/9/dataset_389b778e-00bb-4d28-b79a-c44c182d94db.dat' -o 'out1.fq' 'cutadapt_small_fastq.fq' > report.txt", "user_email": "tests@fake.org", "command_version": null, "params": {"library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 28, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "output_selector": "[\"report\", \"info_file\"]", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"library|input_1": {"id": "a6dc655213a10cb8", "src": "hda", "uuid": "57b443b6-2449-4c1e-940d-705244af818a"}}, "outputs": {"out1": {"id": "02ee2ca586d13cce", "src": "hda", "uuid": "6412f1a4-e291-47df-932e-bcb2c7d47fe1"}, "report": {"id": "a9473ff78ba6571a", "src": "hda", "uuid": "8ff16f52-2b79-446d-a011-55c20adfe29e"}, "info_file": {"id": "df0cf971a23d18a1", "src": "hda", "uuid": "389b778e-00bb-4d28-b79a-c44c182d94db"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "cutadapt/4.9+galaxy1-9", "has_data": true, "data": {"tool_id": "cutadapt", "tool_version": "4.9+galaxy1", "test_index": 9, "time_seconds": 33.915284395217896, "inputs": {"library|input_1": {"src": "hda", "id": "a71f6c5d72119bc6"}, "library|r1|adapters_0|adapter_source|adapter": "AGATCGGAAGAGC", "library|r1|adapters_0|adapter_source|adapter_source_list": "user", "library|type": "single", "output_selector": ["report", "info_file"]}, "job": {"model_class": "Job", "id": "06ad6eb972ef127c", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:59:08.579043", "update_time": "2024-09-23T06:59:22.531411", "galaxy_version": "24.1", "external_id": "gxy-d2xh2", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/c/e/c/dataset_cec6e455-e925-41c8-aa87-c453bcc9d78f.dat' 'cutadapt_small_fastq.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 --info-file='/galaxy/server/database/objects/2/e/3/dataset_2e3eb281-5388-4407-bc94-d0d3ce471985.dat' -o 'out1.fq' 'cutadapt_small_fastq.fq' > report.txt", "user_email": "tests@fake.org", "command_version": "4.9", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_selector": "[\"report\", \"info_file\"]", "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 157, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"type\": \"single\"}"}, "inputs": {"library|input_1": {"id": "a71f6c5d72119bc6", "src": "hda", "uuid": "cec6e455-e925-41c8-aa87-c453bcc9d78f"}}, "outputs": {"out1": {"id": "58530ce64817ca02", "src": "hda", "uuid": "6aaad4fb-22fb-4e46-9607-accbe379ebfc"}, "report": {"id": "4530f5677a812594", "src": "hda", "uuid": "b5242ab2-77b6-4b25-8787-e785d8714e4d"}, "info_file": {"id": "641bfcc3d43b0b9e", "src": "hda", "uuid": "2e3eb281-5388-4407-bc94-d0d3ce471985"}}, "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": "2024-09-23 06:59:11", "plugin": "core", "name": "end_epoch", "raw_value": "1727074751.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:59:10", "plugin": "core", "name": "start_epoch", "raw_value": "1727074750.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_compare/3.5.4+galaxy0-0", "has_data": true, "data": {"tool_id": "deeptools_bam_compare", "tool_version": "3.5.4+galaxy0", "test_index": 0, "time_seconds": 79.64213180541992, "inputs": {"bamFile1": {"src": "hda", "id": "abbc0a781ea0cf97"}, "bamFile2": {"src": "hda", "id": "abbc0a781ea0cf97"}, "binSize": "5", "comparison|type": "ratio", "outFileFormat": "bedgraph", "advancedOpt|showAdvancedOpt": "no"}, "job": {"model_class": "Job", "id": "c75fb1819c3bf55e", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:27:47.558007", "update_time": "2024-09-23T06:28:39.518059", "galaxy_version": "24.1", "external_id": "gxy-pkcqg", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/e/e/8/dataset_ee8780d3-30dc-4ba9-92ae-d93a15553776.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/2/c/c/metadata_2ccd0acd-ec8b-4f6c-9951-858110cddacb.dat' one.bam.bai && ln -s '/galaxy/server/database/objects/e/e/8/dataset_ee8780d3-30dc-4ba9-92ae-d93a15553776.dat' two.bam && ln -s '/galaxy/server/database/objects/_metadata_files/2/c/c/metadata_2ccd0acd-ec8b-4f6c-9951-858110cddacb.dat' two.bam.bai && bamCompare --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bamfile1 one.bam --bamfile2 two.bam --outFileName '/galaxy/server/database/objects/5/8/7/dataset_587184d2-65be-471f-99c8-c4c73afa8cce.dat' --outFileFormat 'bedgraph' --binSize 5 --scaleFactorsMethod readCount --operation ratio --pseudocount 1 1", "user_email": "tests@fake.org", "command_version": "bamCompare 3.5.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "region": "\"\"", "outFileFormat": "\"bedgraph\"", "exactScaling": "false", "comparison": "{\"__current_case__\": 1, \"pseudocount\": \"1 1\", \"type\": \"ratio\"}", "scaling": "{\"__current_case__\": 1, \"method\": \"readCount\"}", "binSize": "\"5\""}, "inputs": {"bamFile2": {"id": "abbc0a781ea0cf97", "src": "hda", "uuid": "ee8780d3-30dc-4ba9-92ae-d93a15553776"}, "bamFile1": {"id": "abbc0a781ea0cf97", "src": "hda", "uuid": "ee8780d3-30dc-4ba9-92ae-d93a15553776"}}, "outputs": {"outFileName": {"id": "c75fb1819c3bf55e", "src": "hda", "uuid": "587184d2-65be-471f-99c8-c4c73afa8cce"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "bamFilesList: ['one.bam', 'two.bam']\nbinLength: 5\nnumberOfSamples: 0\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 5\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "bamFilesList: ['one.bam', 'two.bam']\nbinLength: 5\nnumberOfSamples: 0\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 5\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:28:25", "plugin": "core", "name": "end_epoch", "raw_value": "1727072905.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:28:24", "plugin": "core", "name": "start_epoch", "raw_value": "1727072904.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_compare/3.5.4+galaxy0-1", "has_data": true, "data": {"tool_id": "deeptools_bam_compare", "tool_version": "3.5.4+galaxy0", "test_index": 1, "time_seconds": 34.28258514404297, "inputs": {"bamFile1": {"src": "hda", "id": "92eb80a7dc7367fd"}, "bamFile2": {"src": "hda", "id": "92eb80a7dc7367fd"}, "binSize": "10", "comparison|type": "ratio", "outFileFormat": "bigwig", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "376b402441ccf867", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T06:28:59.763034", "update_time": "2024-09-23T06:29:13.938854", "galaxy_version": "24.1", "external_id": "gxy-zjdks", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/a/4/e/dataset_a4ed11ab-fad9-498c-a321-d7ba4a528500.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/3/4/0/metadata_34047d3f-8812-478e-86bf-b3790043b604.dat' one.bam.bai && ln -s '/galaxy/server/database/objects/a/4/e/dataset_a4ed11ab-fad9-498c-a321-d7ba4a528500.dat' two.bam && ln -s '/galaxy/server/database/objects/_metadata_files/3/4/0/metadata_34047d3f-8812-478e-86bf-b3790043b604.dat' two.bam.bai && bamCompare --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bamfile1 one.bam --bamfile2 two.bam --outFileName '/galaxy/server/database/objects/0/2/f/dataset_02f1b284-2261-4052-a3aa-b216539e4680.dat' --outFileFormat 'bigwig' --binSize 10 --scaleFactorsMethod readCount --operation ratio --pseudocount 1 1 --minMappingQuality '1'", "user_email": "tests@fake.org", "command_version": "bamCompare 3.5.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 1, \"blackListFileName\": null, \"centerReads\": false, \"doExtendCustom\": {\"__current_case__\": 0, \"doExtend\": \"no\"}, \"ignoreDuplicates\": false, \"ignoreForNormalization\": \"\", \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"1\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"showAdvancedOpt\": \"yes\", \"skipNAs\": false, \"skipZeroOverZero\": \"\", \"smoothLength\": \"\"}", "region": "\"\"", "outFileFormat": "\"bigwig\"", "exactScaling": "false", "comparison": "{\"__current_case__\": 1, \"pseudocount\": \"1 1\", \"type\": \"ratio\"}", "scaling": "{\"__current_case__\": 1, \"method\": \"readCount\"}", "binSize": "\"10\""}, "inputs": {"bamFile2": {"id": "92eb80a7dc7367fd", "src": "hda", "uuid": "a4ed11ab-fad9-498c-a321-d7ba4a528500"}, "bamFile1": {"id": "92eb80a7dc7367fd", "src": "hda", "uuid": "a4ed11ab-fad9-498c-a321-d7ba4a528500"}}, "outputs": {"outFileName": {"id": "376b402441ccf867", "src": "hda", "uuid": "02f1b284-2261-4052-a3aa-b216539e4680"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Due to filtering, 83.33333333333334% of the aforementioned alignments will be used 39.16666666666667\nDue to filtering, 83.33333333333334% of the aforementioned alignments will be used 39.16666666666667\n", "tool_stderr": "bamFilesList: ['one.bam', 'two.bam']\nbinLength: 10\nnumberOfSamples: 0\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: 1\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stdout": "Due to filtering, 83.33333333333334% of the aforementioned alignments will be used 39.16666666666667\nDue to filtering, 83.33333333333334% of the aforementioned alignments will be used 39.16666666666667\n", "stderr": "bamFilesList: ['one.bam', 'two.bam']\nbinLength: 10\nnumberOfSamples: 0\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: 1\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-23 06:29:02", "plugin": "core", "name": "end_epoch", "raw_value": "1727072942.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 06:29:01", "plugin": "core", "name": "start_epoch", "raw_value": "1727072941.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "dropletutils_read_10x/1.0.4+galaxy0-0", "has_data": true, "data": {"tool_id": "dropletutils_read_10x", "tool_version": "1.0.4+galaxy0", "test_index": 0, "time_seconds": 0.22600769996643066, "execution_problem": "Input staging problem: Test input file (matrix.mtx) cannot be found.", "status": "error"}}, {"id": "fastqc/0.74+galaxy1-0", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 0, "time_seconds": 49.57119083404541, "inputs": {"input_file": {"src": "hda", "id": "cf4a5f1219ef1fa0"}}, "job": {"model_class": "Job", "id": "2dcbbe31c83616e8", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:19:18.130047", "update_time": "2024-09-23T07:19:45.935867", "galaxy_version": "24.1", "external_id": "gxy-w8f2g", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/1/3/9/dataset_139aac29-e3b1-40a2-a6aa-54a3258fde61.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/7/8/0/dataset_7805692b-f2df-42dc-ab78-3c0de051866d_files' && fastqc --outdir '/galaxy/server/database/objects/7/8/0/dataset_7805692b-f2df-42dc-ab78-3c0de051866d_files' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/7/8/0/dataset_7805692b-f2df-42dc-ab78-3c0de051866d_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/7/8/0/dataset_7805692b-f2df-42dc-ab78-3c0de051866d_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"7\"", "min_length": "\"\"", "nogroup": "false", "limits": null, "adapters": null, "contaminants": null}, "inputs": {"input_file": {"id": "cf4a5f1219ef1fa0", "src": "hda", "uuid": "139aac29-e3b1-40a2-a6aa-54a3258fde61"}}, "outputs": {"html_file": {"id": "3192f63e428f6a43", "src": "hda", "uuid": "7805692b-f2df-42dc-ab78-3c0de051866d"}, "text_file": {"id": "6701fc90ee737b9f", "src": "hda", "uuid": "36cccaef-a192-459e-ad1d-a2382c2908f4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "null\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "null\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:19:31", "plugin": "core", "name": "end_epoch", "raw_value": "1727075971.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:19:29", "plugin": "core", "name": "start_epoch", "raw_value": "1727075969.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.74+galaxy1-0", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 0, "time_seconds": 38.480724811553955, "inputs": {"input_file": {"src": "hda", "id": "a8a0896582d6267b"}}, "job": {"model_class": "Job", "id": "121d75de73994175", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:23:37.182511", "update_time": "2024-09-23T07:23:54.047337", "galaxy_version": "24.1", "external_id": "gxy-d5lr4", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/a/e/dataset_caec1d58-91e7-4d24-8338-60c3f5e37fbb.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/d/f/c/dataset_dfc64775-5669-4d90-82f9-409c72804deb_files' && fastqc --outdir '/galaxy/server/database/objects/d/f/c/dataset_dfc64775-5669-4d90-82f9-409c72804deb_files' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/d/f/c/dataset_dfc64775-5669-4d90-82f9-409c72804deb_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/d/f/c/dataset_dfc64775-5669-4d90-82f9-409c72804deb_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"7\"", "min_length": "\"\"", "nogroup": "false", "limits": null, "adapters": null, "contaminants": null}, "inputs": {"input_file": {"id": "a8a0896582d6267b", "src": "hda", "uuid": "caec1d58-91e7-4d24-8338-60c3f5e37fbb"}}, "outputs": {"html_file": {"id": "bdc88e9437af602c", "src": "hda", "uuid": "dfc64775-5669-4d90-82f9-409c72804deb"}, "text_file": {"id": "6b28484e5755691b", "src": "hda", "uuid": "d219985c-bf10-4fe2-ab85-fc2d7df1acd3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "null\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "null\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:23:42", "plugin": "core", "name": "end_epoch", "raw_value": "1727076222.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:23:39", "plugin": "core", "name": "start_epoch", "raw_value": "1727076219.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.74+galaxy1-1", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 1, "time_seconds": 38.29883337020874, "inputs": {"input_file": {"src": "hda", "id": "edba7dac7ef7c78e"}, "contaminants": {"src": "hda", "id": "98743993a60a134d"}}, "job": {"model_class": "Job", "id": "c79b33f10299ee40", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:20:07.346287", "update_time": "2024-09-23T07:20:24.087391", "galaxy_version": "24.1", "external_id": "gxy-ph742", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/4/5/e/dataset_45e347f0-3afc-4c1c-8052-e106d222ebad.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/b/b/4/dataset_bb4d07f9-6456-4958-82ec-736b01a19e02_files' && fastqc --outdir '/galaxy/server/database/objects/b/b/4/dataset_bb4d07f9-6456-4958-82ec-736b01a19e02_files' --contaminants '/galaxy/server/database/objects/2/b/1/dataset_2b171e14-fe33-45ac-8293-0ef440dfd852.dat' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/b/b/4/dataset_bb4d07f9-6456-4958-82ec-736b01a19e02_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/b/b/4/dataset_bb4d07f9-6456-4958-82ec-736b01a19e02_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"7\"", "min_length": "\"\"", "nogroup": "false", "limits": null, "adapters": null}, "inputs": {"input_file": {"id": "edba7dac7ef7c78e", "src": "hda", "uuid": "45e347f0-3afc-4c1c-8052-e106d222ebad"}, "contaminants": {"id": "98743993a60a134d", "src": "hda", "uuid": "2b171e14-fe33-45ac-8293-0ef440dfd852"}}, "outputs": {"html_file": {"id": "b887fa8965effbaa", "src": "hda", "uuid": "bb4d07f9-6456-4958-82ec-736b01a19e02"}, "text_file": {"id": "67e4d62250358c59", "src": "hda", "uuid": "914ec297-95fe-4e8c-8f97-34e59643414a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "null\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "null\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:20:13", "plugin": "core", "name": "end_epoch", "raw_value": "1727076013.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:20:10", "plugin": "core", "name": "start_epoch", "raw_value": "1727076010.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.74+galaxy1-1", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 1, "time_seconds": 11.361786603927612, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "fastqc/0.74+galaxy1-2", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 2, "time_seconds": 36.490092277526855, "inputs": {"input_file": {"src": "hda", "id": "3745fb82b25c4f91"}, "adapters": {"src": "hda", "id": "fd877d819abcee48"}}, "job": {"model_class": "Job", "id": "0faed797a64c6f5c", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:20:45.795668", "update_time": "2024-09-23T07:21:00.659924", "galaxy_version": "24.1", "external_id": "gxy-6fm2m", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/e/5/f/dataset_e5f6acc3-5852-480d-a9ac-acf0f638f55b.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/b/d/e/dataset_bde19f54-f743-4da1-b141-73c477f8e968_files' && fastqc --outdir '/galaxy/server/database/objects/b/d/e/dataset_bde19f54-f743-4da1-b141-73c477f8e968_files' --adapters '/galaxy/server/database/objects/f/7/6/dataset_f7654ad1-bbde-4a7b-8bf2-3c25b405f0f5.dat' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/b/d/e/dataset_bde19f54-f743-4da1-b141-73c477f8e968_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/b/d/e/dataset_bde19f54-f743-4da1-b141-73c477f8e968_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"7\"", "min_length": "\"\"", "nogroup": "false", "limits": null, "contaminants": null}, "inputs": {"input_file": {"id": "3745fb82b25c4f91", "src": "hda", "uuid": "e5f6acc3-5852-480d-a9ac-acf0f638f55b"}, "adapters": {"id": "fd877d819abcee48", "src": "hda", "uuid": "f7654ad1-bbde-4a7b-8bf2-3c25b405f0f5"}}, "outputs": {"html_file": {"id": "320e522d4adab311", "src": "hda", "uuid": "bde19f54-f743-4da1-b141-73c477f8e968"}, "text_file": {"id": "0a794115be35a40a", "src": "hda", "uuid": "11036291-1b1f-4800-94f1-d981fefb8990"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "null\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "null\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:20:49", "plugin": "core", "name": "end_epoch", "raw_value": "1727076049.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:20:47", "plugin": "core", "name": "start_epoch", "raw_value": "1727076047.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.74+galaxy1-2", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 2, "time_seconds": 37.985180139541626, "inputs": {"input_file": {"src": "hda", "id": "94eb51fbeee9c3e3"}, "adapters": {"src": "hda", "id": "cc98b54f0d8e0381"}}, "job": {"model_class": "Job", "id": "c7fe15621a9f268d", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:24:27.630756", "update_time": "2024-09-23T07:24:43.358794", "galaxy_version": "24.1", "external_id": "gxy-rjcvl", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/0/0/2/dataset_002a789d-fa2c-4038-a2f6-f0b467fe846e.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/3/3/3/dataset_3332632f-7081-41ef-9a15-ed6202c25ba6_files' && fastqc --outdir '/galaxy/server/database/objects/3/3/3/dataset_3332632f-7081-41ef-9a15-ed6202c25ba6_files' --adapters '/galaxy/server/database/objects/4/7/3/dataset_47370a7e-de62-44e7-89f6-53f0798d85a2.dat' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/3/3/3/dataset_3332632f-7081-41ef-9a15-ed6202c25ba6_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/3/3/3/dataset_3332632f-7081-41ef-9a15-ed6202c25ba6_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"7\"", "min_length": "\"\"", "nogroup": "false", "limits": null, "contaminants": null}, "inputs": {"input_file": {"id": "94eb51fbeee9c3e3", "src": "hda", "uuid": "002a789d-fa2c-4038-a2f6-f0b467fe846e"}, "adapters": {"id": "cc98b54f0d8e0381", "src": "hda", "uuid": "47370a7e-de62-44e7-89f6-53f0798d85a2"}}, "outputs": {"html_file": {"id": "863f314e05b4c29d", "src": "hda", "uuid": "3332632f-7081-41ef-9a15-ed6202c25ba6"}, "text_file": {"id": "a4947d1fb3e68781", "src": "hda", "uuid": "fb51d778-714b-43e0-baa0-63003e8f6e2e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "null\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "null\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:24:31", "plugin": "core", "name": "end_epoch", "raw_value": "1727076271.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:24:29", "plugin": "core", "name": "start_epoch", "raw_value": "1727076269.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.74+galaxy1-3", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 3, "time_seconds": 36.49792122840881, "inputs": {"input_file": {"src": "hda", "id": "15c515aedae028a5"}, "limits": {"src": "hda", "id": "6fa2df4c710d9e61"}}, "job": {"model_class": "Job", "id": "2a78b53ebc84fd37", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:21:21.777589", "update_time": "2024-09-23T07:21:37.405444", "galaxy_version": "24.1", "external_id": "gxy-nkvq8", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/2/d/f/dataset_2df4c628-b593-45dc-928f-9f578b7a5305.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/9/1/b/dataset_91b06dae-14b0-4cc7-be53-2d47d3dfcc3e_files' && fastqc --outdir '/galaxy/server/database/objects/9/1/b/dataset_91b06dae-14b0-4cc7-be53-2d47d3dfcc3e_files' --limits '/galaxy/server/database/objects/b/2/8/dataset_b289bd3c-f4b9-4a3b-ba7c-f997c58604ba.dat' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/9/1/b/dataset_91b06dae-14b0-4cc7-be53-2d47d3dfcc3e_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/9/1/b/dataset_91b06dae-14b0-4cc7-be53-2d47d3dfcc3e_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"7\"", "min_length": "\"\"", "nogroup": "false", "adapters": null, "contaminants": null}, "inputs": {"input_file": {"id": "15c515aedae028a5", "src": "hda", "uuid": "2df4c628-b593-45dc-928f-9f578b7a5305"}, "limits": {"id": "6fa2df4c710d9e61", "src": "hda", "uuid": "b289bd3c-f4b9-4a3b-ba7c-f997c58604ba"}}, "outputs": {"html_file": {"id": "323568a6be413f81", "src": "hda", "uuid": "91b06dae-14b0-4cc7-be53-2d47d3dfcc3e"}, "text_file": {"id": "dd08e6354119fae5", "src": "hda", "uuid": "66e2fe05-1520-45d3-a327-f88a17571ad3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "null\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "null\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:21:26", "plugin": "core", "name": "end_epoch", "raw_value": "1727076086.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:21:24", "plugin": "core", "name": "start_epoch", "raw_value": "1727076084.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.74+galaxy1-3", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 3, "time_seconds": 37.532058000564575, "inputs": {"input_file": {"src": "hda", "id": "6520e1f6478ad976"}, "limits": {"src": "hda", "id": "5753ffedd3b75081"}}, "job": {"model_class": "Job", "id": "272286992fb506bb", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:25:05.653355", "update_time": "2024-09-23T07:25:21.046475", "galaxy_version": "24.1", "external_id": "gxy-447lt", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/7/f/3/dataset_7f3b63ee-3240-4862-8521-0e277c9d8198.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/b/b/3/dataset_bb3db393-5462-4651-9e94-c8a79b66490b_files' && fastqc --outdir '/galaxy/server/database/objects/b/b/3/dataset_bb3db393-5462-4651-9e94-c8a79b66490b_files' --limits '/galaxy/server/database/objects/b/3/3/dataset_b3332e37-014f-4e2e-bbf9-940260d4d7f4.dat' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/b/b/3/dataset_bb3db393-5462-4651-9e94-c8a79b66490b_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/b/b/3/dataset_bb3db393-5462-4651-9e94-c8a79b66490b_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"7\"", "min_length": "\"\"", "nogroup": "false", "adapters": null, "contaminants": null}, "inputs": {"input_file": {"id": "6520e1f6478ad976", "src": "hda", "uuid": "7f3b63ee-3240-4862-8521-0e277c9d8198"}, "limits": {"id": "5753ffedd3b75081", "src": "hda", "uuid": "b3332e37-014f-4e2e-bbf9-940260d4d7f4"}}, "outputs": {"html_file": {"id": "ae7a4da46530b584", "src": "hda", "uuid": "bb3db393-5462-4651-9e94-c8a79b66490b"}, "text_file": {"id": "87c20641f835b9b7", "src": "hda", "uuid": "f96cfb14-68ac-439a-9db5-518ced5bf215"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "null\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "null\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:25:09", "plugin": "core", "name": "end_epoch", "raw_value": "1727076309.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:25:07", "plugin": "core", "name": "start_epoch", "raw_value": "1727076307.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.74+galaxy1-4", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 4, "time_seconds": 11.97918963432312, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "fastqc/0.74+galaxy1-4", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 4, "time_seconds": 38.39649248123169, "inputs": {"input_file": {"src": "hda", "id": "5148067aa6ded308"}, "limits": {"src": "hda", "id": "654fbcfb9e64af94"}, "kmers": "3"}, "job": {"model_class": "Job", "id": "983882a617d10737", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:25:43.460242", "update_time": "2024-09-23T07:25:59.544148", "galaxy_version": "24.1", "external_id": "gxy-2vxqm", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/b/3/6/dataset_b360c8f4-df73-47f0-8f76-ca21208617cc.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/7/6/9/dataset_769878e7-d7b6-42b3-a42d-c8f52908b41f_files' && fastqc --outdir '/galaxy/server/database/objects/7/6/9/dataset_769878e7-d7b6-42b3-a42d-c8f52908b41f_files' --limits '/galaxy/server/database/objects/8/1/f/dataset_81fa0795-6cab-4324-8266-8d6c0d7025c4.dat' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --kmers 3 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/7/6/9/dataset_769878e7-d7b6-42b3-a42d-c8f52908b41f_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/7/6/9/dataset_769878e7-d7b6-42b3-a42d-c8f52908b41f_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"3\"", "min_length": "\"\"", "nogroup": "false", "adapters": null, "contaminants": null}, "inputs": {"input_file": {"id": "5148067aa6ded308", "src": "hda", "uuid": "b360c8f4-df73-47f0-8f76-ca21208617cc"}, "limits": {"id": "654fbcfb9e64af94", "src": "hda", "uuid": "81fa0795-6cab-4324-8266-8d6c0d7025c4"}}, "outputs": {"html_file": {"id": "210169297ad96e00", "src": "hda", "uuid": "769878e7-d7b6-42b3-a42d-c8f52908b41f"}, "text_file": {"id": "8c3d34315d165182", "src": "hda", "uuid": "266e594b-d9d7-4994-b4b6-10166a5f4d18"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "null\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "null\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:25:47", "plugin": "core", "name": "end_epoch", "raw_value": "1727076347.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:25:45", "plugin": "core", "name": "start_epoch", "raw_value": "1727076345.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.74+galaxy1-5", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 5, "time_seconds": 37.44086956977844, "inputs": {"input_file": {"src": "hda", "id": "2479e8ebff9ce8ef"}, "min_length": "108"}, "job": {"model_class": "Job", "id": "3f96099cf1b666e9", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:22:11.338307", "update_time": "2024-09-23T07:22:26.810113", "galaxy_version": "24.1", "external_id": "gxy-rsj9w", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/6/2/f/dataset_62f00ea1-48b2-44f6-aade-0295b689669a.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/e/4/5/dataset_e458b19d-058f-4691-90c3-28416f2481e7_files' && fastqc --outdir '/galaxy/server/database/objects/e/4/5/dataset_e458b19d-058f-4691-90c3-28416f2481e7_files' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --min_length 108 --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/e/4/5/dataset_e458b19d-058f-4691-90c3-28416f2481e7_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/e/4/5/dataset_e458b19d-058f-4691-90c3-28416f2481e7_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"7\"", "min_length": "\"108\"", "nogroup": "false", "limits": null, "adapters": null, "contaminants": null}, "inputs": {"input_file": {"id": "2479e8ebff9ce8ef", "src": "hda", "uuid": "62f00ea1-48b2-44f6-aade-0295b689669a"}}, "outputs": {"html_file": {"id": "acbce4dc27fa974b", "src": "hda", "uuid": "e458b19d-058f-4691-90c3-28416f2481e7"}, "text_file": {"id": "78d567e71ed12653", "src": "hda", "uuid": "d61c0f0b-decc-4f9a-b5c7-91084af73878"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "null\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "null\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:22:15", "plugin": "core", "name": "end_epoch", "raw_value": "1727076135.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:22:13", "plugin": "core", "name": "start_epoch", "raw_value": "1727076133.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.74+galaxy1-5", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 5, "time_seconds": 38.095070123672485, "inputs": {"input_file": {"src": "hda", "id": "763ed8a056a24ed9"}, "min_length": "108"}, "job": {"model_class": "Job", "id": "5c8f33675f7c28a2", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:26:21.948478", "update_time": "2024-09-23T07:26:37.844421", "galaxy_version": "24.1", "external_id": "gxy-jwb7s", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/c/8/dataset_cc8942a2-abfe-4db1-b16d-64ae31d1a88f.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/7/3/e/dataset_73ef42f0-6b1f-409d-ab07-c47aa4501ca5_files' && fastqc --outdir '/galaxy/server/database/objects/7/3/e/dataset_73ef42f0-6b1f-409d-ab07-c47aa4501ca5_files' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --min_length 108 --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/7/3/e/dataset_73ef42f0-6b1f-409d-ab07-c47aa4501ca5_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/7/3/e/dataset_73ef42f0-6b1f-409d-ab07-c47aa4501ca5_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"7\"", "min_length": "\"108\"", "nogroup": "false", "limits": null, "adapters": null, "contaminants": null}, "inputs": {"input_file": {"id": "763ed8a056a24ed9", "src": "hda", "uuid": "cc8942a2-abfe-4db1-b16d-64ae31d1a88f"}}, "outputs": {"html_file": {"id": "5b2bf096077bd243", "src": "hda", "uuid": "73ef42f0-6b1f-409d-ab07-c47aa4501ca5"}, "text_file": {"id": "d42a9ebc0801e970", "src": "hda", "uuid": "95f47002-a61a-46af-b0db-175ba3d072bd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "null\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "null\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime 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"data": {"tool_id": "fastqc", "tool_version": "0.74+galaxy1", "test_index": 6, "time_seconds": 37.93000316619873, "inputs": {"input_file": {"src": "hda", "id": "84154a63c3485b7a"}, "nogroup": true}, "job": {"model_class": "Job", "id": "df4da4e0e70a7cba", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:26:59.198757", "update_time": "2024-09-23T07:27:15.829444", "galaxy_version": "24.1", "external_id": "gxy-9dcjw", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/6/f/f/dataset_6ff5e23f-8daf-4787-85dd-0c6646dc7454.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/e/a/3/dataset_ea3283e6-fbcb-4f9e-b84c-5c8cdaf2cb6a_files' && fastqc --outdir '/galaxy/server/database/objects/e/a/3/dataset_ea3283e6-fbcb-4f9e-b84c-5c8cdaf2cb6a_files' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --nogroup --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/e/a/3/dataset_ea3283e6-fbcb-4f9e-b84c-5c8cdaf2cb6a_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/e/a/3/dataset_ea3283e6-fbcb-4f9e-b84c-5c8cdaf2cb6a_files'/*\\.html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "kmers": "\"7\"", "min_length": "\"\"", "nogroup": "true", "limits": null, "adapters": null, "contaminants": null}, "inputs": {"input_file": {"id": "84154a63c3485b7a", "src": "hda", "uuid": "6ff5e23f-8daf-4787-85dd-0c6646dc7454"}}, "outputs": {"html_file": {"id": "c78b432e4d833a49", "src": "hda", "uuid": "ea3283e6-fbcb-4f9e-b84c-5c8cdaf2cb6a"}, "text_file": {"id": "56984c4dd095505f", "src": "hda", "uuid": "01880a30-dbfb-407a-8f21-8714e955c116"}}, "copied_from_job_id": null, "output_collections": 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36.34331464767456, "inputs": {"input_file": {"src": "hda", "id": "2f57da5451814566"}}, "job": {"model_class": "Job", "id": "9e3f9bfea79b9451", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:22:59.545336", "update_time": "2024-09-23T07:23:14.649993", "galaxy_version": "24.1", "external_id": "gxy-hgrrw", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/3/1/dataset_c3189488-a233-474c-9ddc-afdac5a5f175.dat' 'hisat_output_1_bam' && mkdir -p '/galaxy/server/database/objects/b/e/e/dataset_bee54795-ef17-47d3-80c1-ad6d434a8710_files' && fastqc --outdir '/galaxy/server/database/objects/b/e/e/dataset_bee54795-ef17-47d3-80c1-ad6d434a8710_files' --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract --kmers 7 -f 'bam' 'hisat_output_1_bam' && cp 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"command_version": "", "params": {"__input_ext": "\"json\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "tsv": "true", "filter": "\".[] | [.foo, .bar]\""}, "inputs": {"input": {"id": "d9be7c2b83ab02a6", "src": "hda", "uuid": "702fb386-0855-47fa-92ba-6524694bdd6b"}}, "outputs": {"output": {"id": "13a085c7d7aeb5d1", "src": "hda", "uuid": "fa7955d7-9b70-4c20-972b-3415f34e29d4"}}, "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": "2024-09-23 08:05:22", "plugin": "core", "name": "end_epoch", "raw_value": "1727078722.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:05:22", "plugin": "core", "name": "start_epoch", 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'/galaxy/server/database/objects/3/9/6/dataset_3969aa18-80bc-4c7c-b233-20dd75902089.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "num_bins": "\"50\"", "max_length": "\"1000000000\"", "min_length": "\"0\"", "theme_bw": "false", "extension": "\"pdf\""}, "inputs": {"input": {"id": "fca5fc051c4ad73e", "src": "hda", "uuid": "0cbaba6f-e05d-46fe-93ef-ef71c3963030"}}, "outputs": {"output": {"id": "1911e35313353edc", "src": "hda", "uuid": "3969aa18-80bc-4c7c-b233-20dd75902089"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, exit_code: None, stderr: 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--max-length 1000000000 --num-bins 50 && mv histogram.svg '/galaxy/server/database/objects/b/b/b/dataset_bbb8503c-b752-4b71-80fb-36c405f0d7ce.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "num_bins": "\"50\"", "max_length": "\"1000000000\"", "min_length": "\"0\"", "theme_bw": "false", "extension": "\"svg\""}, "inputs": {"input": {"id": "3bf666a8b34bc248", "src": "hda", "uuid": "f3eb6aea-2695-4312-9299-ed5156173a06"}}, "outputs": {"output": {"id": "e07ca870e581a4b1", "src": "hda", "uuid": "bbb8503c-b752-4b71-80fb-36c405f0d7ce"}}, "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": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:47:44", "plugin": "core", "name": "end_epoch", "raw_value": "1727077664.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:47:41", "plugin": "core", "name": "start_epoch", "raw_value": "1727077661.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "rna_starsolo/2.7.8a-0", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 0, "time_seconds": 108.54211378097534, "inputs": {"refGenomeSource|genomeFastaFiles": {"src": "hda", "id": "7faec5875443c803"}, "refGenomeSource|genomeSAindexNbases": "4", "refGenomeSource|sjdbGTFfile": {"src": "hda", "id": "b9fca5aed71d03fe"}, "refGenomeSource|sjdbOverhang": "100", "refGenomeSource|geneSource": "history", "sc|input_types|input1": {"src": "hda", "id": "2334768aa7fd2c43"}, "sc|input_types|input2": {"src": "hda", "id": "8707e9b64a16f537"}, "sc|input_types|use": "repeat", "sc|soloCBwhitelist": {"src": "hda", "id": "1852ee4c04a25f99"}, "sc|params|chemistry": "CR3", "sc|soloUMIdedup": "1MM_All", "sc|solo_type": "CB_UMI_Simple", "solo|soloStrand": "Forward", "solo|soloFeatures": "Gene", "solo|filter|filter_type": "no_filter"}, "job": {"model_class": "Job", "id": "38568f59e23ee481", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:28:05.897404", "update_time": "2024-09-23T07:29:16.388259", "galaxy_version": "24.1", "external_id": "gxy-ptmhr", "handler": null, "job_runner_name": null, "command_line": "mkdir -p tempstargenomedir && STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' --genomeFastaFiles '/galaxy/server/database/objects/e/1/b/dataset_e1b6c4f0-4036-4139-82df-af9f1125f121.dat' --sjdbOverhang '100' --sjdbGTFfile '/galaxy/server/database/objects/c/e/d/dataset_ced1d969-60d8-4683-a20f-3451bb8ff058.dat' --genomeSAindexNbases 4 --runThreadN ${GALAXY_SLOTS:-4} && STAR --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --soloType CB_UMI_Simple --readFilesIn /galaxy/server/database/objects/f/e/0/dataset_fe00f1dc-5771-4995-b550-544a417eece4.dat /galaxy/server/database/objects/1/0/b/dataset_10b43612-051c-420d-a4e6-f0d01d0f0810.dat --soloCBmatchWLtype 1MM_multi --readFilesCommand zcat --soloCBwhitelist '/galaxy/server/database/objects/6/6/9/dataset_6697b2ba-aa75-4b2e-aaff-c82d189f2153.dat' --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloUMIfiltering - --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_All --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --soloCellFilter None --soloOutFormatFeaturesGeneField3 'Gene Expression' && mv Solo.out/Gene Solo.out/soloFeatures && cat <(echo \"Barcodes:\") Solo.out/Barcodes.stats <(echo \"Genes:\") Solo.out/soloFeatures/Features.stats > '/galaxy/server/database/objects/c/1/e/dataset_c1e36c1f-6f39-44b9-9dee-450391518446.dat' && addthreads=${GALAXY_SLOTS:-2} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/7/c/4/dataset_7c4a2d75-8f6f-482a-8326-c6d8c7397569.dat' Aligned.out.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "solo": "{\"filter\": {\"__current_case__\": 3, \"filter_type\": \"no_filter\"}, \"soloFeatures\": \"Gene\", \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"soloStrand\": \"Forward\", \"soloUMIfiltering\": \"-\"}", "sc": "{\"__current_case__\": 0, \"input_types\": {\"__current_case__\": 0, \"input1\": {\"values\": [{\"id\": 308, \"src\": \"hda\"}]}, \"input2\": {\"values\": [{\"id\": 309, \"src\": \"hda\"}]}, \"use\": \"repeat\"}, \"params\": {\"__current_case__\": 1, \"chemistry\": \"CR3\"}, \"soloBarcodeReadLength\": true, \"soloCBmatchWLtype\": \"1MM_multi\", \"soloCBwhitelist\": {\"values\": [{\"id\": 310, \"src\": \"hda\"}]}, \"soloUMIdedup\": \"1MM_All\", \"solo_type\": \"CB_UMI_Simple\"}", "refGenomeSource": "{\"__current_case__\": 1, \"geneSource\": \"history\", \"genomeFastaFiles\": {\"values\": [{\"id\": 311, \"src\": \"hda\"}]}, \"genomeSAindexNbases\": \"4\", \"sjdbGTFfile\": {\"values\": [{\"id\": 307, \"src\": \"hda\"}]}, \"sjdbOverhang\": \"100\"}"}, "inputs": {"refGenomeSource|genomeFastaFiles": {"id": "b95b92f3a0573edc", "src": "hda", "uuid": "e1b6c4f0-4036-4139-82df-af9f1125f121"}, "refGenomeSource|sjdbGTFfile": {"id": "b9fca5aed71d03fe", "src": "hda", "uuid": "ced1d969-60d8-4683-a20f-3451bb8ff058"}, "sc|input_types|input1": {"id": "2334768aa7fd2c43", "src": "hda", "uuid": "10b43612-051c-420d-a4e6-f0d01d0f0810"}, "sc|input_types|input11": {"id": "2334768aa7fd2c43", "src": "hda", "uuid": "10b43612-051c-420d-a4e6-f0d01d0f0810"}, "sc|input_types|input2": {"id": "8707e9b64a16f537", "src": "hda", "uuid": "fe00f1dc-5771-4995-b550-544a417eece4"}, "sc|input_types|input21": {"id": "8707e9b64a16f537", "src": "hda", "uuid": "fe00f1dc-5771-4995-b550-544a417eece4"}, "sc|soloCBwhitelist": {"id": "1852ee4c04a25f99", "src": "hda", "uuid": "6697b2ba-aa75-4b2e-aaff-c82d189f2153"}}, "outputs": {"output_log": {"id": "f6e266c758e7f989", "src": "hda", "uuid": "00b1cb16-72d4-4efe-9849-e171e46e943e"}, "output_genes": {"id": "0d9569971c18e9df", "src": "hda", "uuid": "03e5b277-8ff4-4357-84ca-8446ddac2ebb"}, "output_barcodes": {"id": "a5067bf732c07e8c", "src": "hda", "uuid": "69bb094b-56cc-45b5-a88b-8f5655027a4c"}, "output_matrix": {"id": "7df1c760b33d3870", "src": "hda", "uuid": "877bcfb9-2788-4e58-9832-1f09edafca33"}, "output_BAM": {"id": "c99502e78aa89fcb", "src": "hda", "uuid": "7c4a2d75-8f6f-482a-8326-c6d8c7397569"}, "output_stats": {"id": "9f3b2ba5273306b0", "src": "hda", "uuid": "c1e36c1f-6f39-44b9-9dee-450391518446"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Sep 23 07:28:46 ..... started STAR run\nSep 23 07:28:46 ... starting to generate Genome files\nSep 23 07:28:46 ..... processing annotations GTF\nSep 23 07:28:46 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:28:46 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:28:46 ... loading chunks from disk, packing SA...\nSep 23 07:28:46 ... finished generating suffix array\nSep 23 07:28:46 ... generating Suffix Array index\nSep 23 07:28:46 ... completed Suffix Array index\nSep 23 07:28:46 ..... inserting junctions into the genome indices\nSep 23 07:28:46 ... writing Genome to disk ...\nSep 23 07:28:46 ... writing Suffix Array to disk ...\nSep 23 07:28:46 ... writing SAindex to disk\nSep 23 07:28:46 ..... finished successfully\nSep 23 07:28:46 ..... started STAR run\nSep 23 07:28:46 ..... loading genome\nSep 23 07:28:46 ..... started mapping\nSep 23 07:29:04 ..... finished mapping\nSep 23 07:29:04 ..... started Solo counting\nSep 23 07:29:04 ..... finished Solo counting\nSep 23 07:29:04 ..... finished successfully\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Sep 23 07:28:46 ..... started STAR run\nSep 23 07:28:46 ... starting to generate Genome files\nSep 23 07:28:46 ..... processing annotations GTF\nSep 23 07:28:46 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:28:46 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:28:46 ... loading chunks from disk, packing SA...\nSep 23 07:28:46 ... finished generating suffix array\nSep 23 07:28:46 ... generating Suffix Array index\nSep 23 07:28:46 ... completed Suffix Array index\nSep 23 07:28:46 ..... inserting junctions into the genome indices\nSep 23 07:28:46 ... writing Genome to disk ...\nSep 23 07:28:46 ... writing Suffix Array to disk ...\nSep 23 07:28:46 ... writing SAindex to disk\nSep 23 07:28:46 ..... finished successfully\nSep 23 07:28:46 ..... started STAR run\nSep 23 07:28:46 ..... loading genome\nSep 23 07:28:46 ..... started mapping\nSep 23 07:29:04 ..... finished mapping\nSep 23 07:29:04 ..... started Solo counting\nSep 23 07:29:04 ..... finished Solo counting\nSep 23 07:29:04 ..... finished successfully\n", "stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "18 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "18.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:29:04", "plugin": "core", "name": "end_epoch", "raw_value": "1727076544.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:28:46", "plugin": "core", "name": "start_epoch", "raw_value": "1727076526.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "rna_starsolo/2.7.8a-0", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 0, "time_seconds": 88.85388112068176, "inputs": {"refGenomeSource|genomeFastaFiles": {"src": "hda", "id": "3a1879d3bba5a690"}, "refGenomeSource|genomeSAindexNbases": "4", "refGenomeSource|sjdbGTFfile": {"src": "hda", "id": "386d0735a5dc86d3"}, "refGenomeSource|sjdbOverhang": "100", "refGenomeSource|geneSource": "history", "sc|input_types|input1": {"src": "hda", "id": "c4bf7ea85523cc4a"}, "sc|input_types|input2": {"src": "hda", "id": "992252542d3a7e8b"}, "sc|input_types|use": "repeat", "sc|soloCBwhitelist": {"src": "hda", "id": "ddae5651e3915a81"}, "sc|params|chemistry": "CR3", "sc|soloUMIdedup": "1MM_All", "sc|solo_type": "CB_UMI_Simple", "solo|soloStrand": "Forward", "solo|soloFeatures": "Gene", "solo|filter|filter_type": "no_filter"}, "job": {"model_class": "Job", "id": "22e9ac217513e982", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:38:12.284462", "update_time": "2024-09-23T07:38:57.616927", "galaxy_version": "24.1", "external_id": "gxy-dlg6c", "handler": null, "job_runner_name": null, "command_line": "mkdir -p tempstargenomedir && STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' --genomeFastaFiles '/galaxy/server/database/objects/9/0/6/dataset_906ce901-a5af-4828-9251-935484d19278.dat' --sjdbOverhang '100' --sjdbGTFfile '/galaxy/server/database/objects/9/5/9/dataset_959a4fea-c1dc-4028-9539-5b626bb95733.dat' --genomeSAindexNbases 4 --runThreadN ${GALAXY_SLOTS:-4} && STAR --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --soloType CB_UMI_Simple --readFilesIn /galaxy/server/database/objects/b/0/f/dataset_b0fcc993-54f4-432f-9c7e-3996b98ca8c6.dat /galaxy/server/database/objects/8/4/9/dataset_849b0bb6-24e8-43a1-80a5-675860bd50f7.dat --soloCBmatchWLtype 1MM_multi --readFilesCommand zcat --soloCBwhitelist '/galaxy/server/database/objects/0/d/7/dataset_0d754ec0-c6b5-4eab-bfa2-8c36f41ae048.dat' --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloUMIfiltering - --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_All --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --soloCellFilter None --soloOutFormatFeaturesGeneField3 'Gene Expression' && mv Solo.out/Gene Solo.out/soloFeatures && cat <(echo \"Barcodes:\") Solo.out/Barcodes.stats <(echo \"Genes:\") Solo.out/soloFeatures/Features.stats > '/galaxy/server/database/objects/0/1/8/dataset_01841cea-0131-4d39-acd6-24700e323d38.dat' && addthreads=${GALAXY_SLOTS:-2} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/6/f/f/dataset_6ff83ac4-1586-49e9-b2a0-f4399439e1cf.dat' Aligned.out.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "solo": "{\"filter\": {\"__current_case__\": 3, \"filter_type\": \"no_filter\"}, \"soloFeatures\": \"Gene\", \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"soloStrand\": \"Forward\", \"soloUMIfiltering\": \"-\"}", "sc": "{\"__current_case__\": 0, \"input_types\": {\"__current_case__\": 0, \"input1\": {\"values\": [{\"id\": 400, \"src\": \"hda\"}]}, \"input2\": {\"values\": [{\"id\": 401, \"src\": \"hda\"}]}, \"use\": \"repeat\"}, \"params\": {\"__current_case__\": 1, \"chemistry\": \"CR3\"}, \"soloBarcodeReadLength\": true, \"soloCBmatchWLtype\": \"1MM_multi\", \"soloCBwhitelist\": {\"values\": [{\"id\": 402, \"src\": \"hda\"}]}, \"soloUMIdedup\": \"1MM_All\", \"solo_type\": \"CB_UMI_Simple\"}", "refGenomeSource": "{\"__current_case__\": 1, \"geneSource\": \"history\", \"genomeFastaFiles\": {\"values\": [{\"id\": 403, \"src\": \"hda\"}]}, \"genomeSAindexNbases\": \"4\", \"sjdbGTFfile\": {\"values\": [{\"id\": 399, \"src\": \"hda\"}]}, \"sjdbOverhang\": \"100\"}"}, "inputs": {"refGenomeSource|genomeFastaFiles": {"id": "c36f7f738e22bab8", "src": "hda", "uuid": "906ce901-a5af-4828-9251-935484d19278"}, "refGenomeSource|sjdbGTFfile": {"id": "386d0735a5dc86d3", "src": "hda", "uuid": "959a4fea-c1dc-4028-9539-5b626bb95733"}, "sc|input_types|input1": {"id": "c4bf7ea85523cc4a", "src": "hda", "uuid": "849b0bb6-24e8-43a1-80a5-675860bd50f7"}, "sc|input_types|input11": {"id": "c4bf7ea85523cc4a", "src": "hda", "uuid": "849b0bb6-24e8-43a1-80a5-675860bd50f7"}, "sc|input_types|input2": {"id": "992252542d3a7e8b", "src": "hda", "uuid": "b0fcc993-54f4-432f-9c7e-3996b98ca8c6"}, "sc|input_types|input21": {"id": "992252542d3a7e8b", "src": "hda", "uuid": "b0fcc993-54f4-432f-9c7e-3996b98ca8c6"}, "sc|soloCBwhitelist": {"id": "ddae5651e3915a81", "src": "hda", "uuid": "0d754ec0-c6b5-4eab-bfa2-8c36f41ae048"}}, "outputs": {"output_stats": {"id": "116983429b28d5c4", "src": "hda", "uuid": "01841cea-0131-4d39-acd6-24700e323d38"}, "output_BAM": {"id": "920b4c75f0c9a10a", "src": "hda", "uuid": "6ff83ac4-1586-49e9-b2a0-f4399439e1cf"}, "output_matrix": {"id": "47fa0a5876f8dd81", "src": "hda", "uuid": "5da1b086-03ea-426f-b9e7-e2c3da020d0d"}, "output_barcodes": {"id": "f4cf0063a73d2c4a", "src": "hda", "uuid": "71052891-2be3-4cda-80b4-c5fbfdacc974"}, "output_genes": {"id": "327c66d5ff3a6469", "src": "hda", "uuid": "1902c932-f9d7-445c-93e2-3e45bf74f8ba"}, "output_log": {"id": "cb4beea1623ad968", "src": "hda", "uuid": "f1ce8d16-d7c3-4028-8aa3-a10955685c09"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Sep 23 07:38:27 ..... started STAR run\nSep 23 07:38:27 ... starting to generate Genome files\nSep 23 07:38:27 ..... processing annotations GTF\nSep 23 07:38:27 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:38:27 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:38:27 ... loading chunks from disk, packing SA...\nSep 23 07:38:28 ... finished generating suffix array\nSep 23 07:38:28 ... generating Suffix Array index\nSep 23 07:38:28 ... completed Suffix Array index\nSep 23 07:38:28 ..... inserting junctions into the genome indices\nSep 23 07:38:28 ... writing Genome to disk ...\nSep 23 07:38:28 ... writing Suffix Array to disk ...\nSep 23 07:38:28 ... writing SAindex to disk\nSep 23 07:38:28 ..... finished successfully\nSep 23 07:38:28 ..... started STAR run\nSep 23 07:38:28 ..... loading genome\nSep 23 07:38:28 ..... started mapping\nSep 23 07:38:46 ..... finished mapping\nSep 23 07:38:46 ..... started Solo counting\nSep 23 07:38:46 ..... finished Solo counting\nSep 23 07:38:46 ..... finished successfully\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Sep 23 07:38:27 ..... started STAR run\nSep 23 07:38:27 ... starting to generate Genome files\nSep 23 07:38:27 ..... processing annotations GTF\nSep 23 07:38:27 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:38:27 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:38:27 ... loading chunks from disk, packing SA...\nSep 23 07:38:28 ... finished generating suffix array\nSep 23 07:38:28 ... generating Suffix Array index\nSep 23 07:38:28 ... completed Suffix Array index\nSep 23 07:38:28 ..... inserting junctions into the genome indices\nSep 23 07:38:28 ... writing Genome to disk ...\nSep 23 07:38:28 ... writing Suffix Array to disk ...\nSep 23 07:38:28 ... writing SAindex to disk\nSep 23 07:38:28 ..... finished successfully\nSep 23 07:38:28 ..... started STAR run\nSep 23 07:38:28 ..... loading genome\nSep 23 07:38:28 ..... started mapping\nSep 23 07:38:46 ..... finished mapping\nSep 23 07:38:46 ..... started Solo counting\nSep 23 07:38:46 ..... finished Solo counting\nSep 23 07:38:46 ..... finished successfully\n", "stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "19.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:38:46", "plugin": "core", "name": "end_epoch", "raw_value": "1727077126.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:38:27", "plugin": "core", "name": "start_epoch", "raw_value": "1727077107.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "rna_starsolo/2.7.8a-1", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 1, "time_seconds": 84.95817637443542, "inputs": {"refGenomeSource|genomeFastaFiles": {"src": "hda", "id": "186e048eed014707"}, "refGenomeSource|genomeSAindexNbases": "4", "refGenomeSource|sjdbGTFfile": {"src": "hda", "id": "22e9ac217513e982"}, "refGenomeSource|sjdbOverhang": "100", "refGenomeSource|geneSource": "history", "sc|input_types|input1": {"src": "hda", "id": "f0608cd40efb51d8"}, "sc|input_types|input2": {"src": "hda", "id": "60609b83166bc323"}, "sc|input_types|use": "repeat", "sc|soloCBwhitelist": {"src": "hda", "id": "b21fb1344711fb0c"}, "sc|params|soloCBstart": "1", "sc|params|soloCBlen": "16", "sc|params|soloUMIstart": "17", "sc|params|soloUMIlen": "12", "sc|params|chemistry": "custom", "sc|solo_type": "CB_UMI_Simple", "solo|soloStrand": "Forward", "solo|soloFeatures": "Gene"}, "job": {"model_class": "Job", "id": "3192f63e428f6a43", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:29:56.550563", "update_time": "2024-09-23T07:30:41.525125", "galaxy_version": "24.1", "external_id": "gxy-r72b6", "handler": null, "job_runner_name": null, "command_line": "mkdir -p tempstargenomedir && STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' --genomeFastaFiles '/galaxy/server/database/objects/4/7/d/dataset_47d34a36-5d51-4930-be8c-f6ff8e52581a.dat' --sjdbOverhang '100' --sjdbGTFfile '/galaxy/server/database/objects/b/b/c/dataset_bbca9e98-564b-431c-ba21-68a4304cc4f0.dat' --genomeSAindexNbases 4 --runThreadN ${GALAXY_SLOTS:-4} && STAR --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --soloType CB_UMI_Simple --readFilesIn /galaxy/server/database/objects/f/8/0/dataset_f8087fb8-40c8-47b1-990b-78214559261f.dat /galaxy/server/database/objects/1/d/e/dataset_1de8718b-8382-4e8d-9b41-9a751f2c3a56.dat --soloCBmatchWLtype 1MM_multi --readFilesCommand zcat --soloCBwhitelist '/galaxy/server/database/objects/e/8/6/dataset_e8684a93-d655-47a1-b18c-efd08b9430bc.dat' --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloAdapterSequence '-' --soloAdapterMismatchesNmax 1 --clipAdapterType Hamming --soloUMIfiltering - --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_All --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --soloCellFilter CellRanger2.2 3000 0.99 10.0 --soloOutFormatFeaturesGeneField3 'Gene Expression' && mv Solo.out/Gene Solo.out/soloFeatures && cat <(echo \"Barcodes:\") Solo.out/Barcodes.stats <(echo \"Genes:\") Solo.out/soloFeatures/Features.stats > '/galaxy/server/database/objects/8/6/5/dataset_86590e09-5319-457c-bc48-4ed0f8dc3831.dat' && addthreads=${GALAXY_SLOTS:-2} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/1/2/6/dataset_1264b47e-05c5-41a1-813c-d9e6c6cdfba8.dat' Aligned.out.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "solo": "{\"filter\": {\"__current_case__\": 0, \"filter_type\": \"cellranger2\", \"max_min_ratio\": \"10.0\", \"max_perc\": \"0.99\", \"n_expected\": \"3000\"}, \"soloFeatures\": \"Gene\", \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"soloStrand\": \"Forward\", \"soloUMIfiltering\": \"-\"}", "sc": "{\"__current_case__\": 0, \"input_types\": {\"__current_case__\": 0, \"input1\": {\"values\": [{\"id\": 320, \"src\": \"hda\"}]}, \"input2\": {\"values\": [{\"id\": 321, \"src\": \"hda\"}]}, \"use\": \"repeat\"}, \"params\": {\"__current_case__\": 2, \"bccdna_mate\": {\"__current_case__\": 0, \"bc_location\": \"other_mate\"}, \"chemistry\": \"custom\", \"clipAdapterType\": \"Hamming\", \"soloAdapterMismatchesNmax\": \"1\", \"soloAdapterSequence\": \"-\", \"soloCBlen\": \"16\", \"soloCBstart\": \"1\", \"soloUMIlen\": \"12\", \"soloUMIstart\": \"17\"}, \"soloBarcodeReadLength\": true, \"soloCBmatchWLtype\": \"1MM_multi\", \"soloCBwhitelist\": {\"values\": [{\"id\": 322, \"src\": \"hda\"}]}, \"soloUMIdedup\": \"1MM_All\", \"solo_type\": \"CB_UMI_Simple\"}", "refGenomeSource": "{\"__current_case__\": 1, \"geneSource\": \"history\", \"genomeFastaFiles\": {\"values\": [{\"id\": 323, \"src\": \"hda\"}]}, \"genomeSAindexNbases\": \"4\", \"sjdbGTFfile\": {\"values\": [{\"id\": 319, \"src\": \"hda\"}]}, \"sjdbOverhang\": \"100\"}"}, "inputs": {"refGenomeSource|genomeFastaFiles": {"id": "73008543c518bec9", "src": "hda", "uuid": "47d34a36-5d51-4930-be8c-f6ff8e52581a"}, "refGenomeSource|sjdbGTFfile": {"id": "22e9ac217513e982", "src": "hda", "uuid": "bbca9e98-564b-431c-ba21-68a4304cc4f0"}, "sc|input_types|input1": {"id": "f0608cd40efb51d8", "src": "hda", "uuid": "1de8718b-8382-4e8d-9b41-9a751f2c3a56"}, "sc|input_types|input11": {"id": "f0608cd40efb51d8", "src": "hda", "uuid": "1de8718b-8382-4e8d-9b41-9a751f2c3a56"}, "sc|input_types|input2": {"id": "60609b83166bc323", "src": "hda", "uuid": "f8087fb8-40c8-47b1-990b-78214559261f"}, "sc|input_types|input21": {"id": "60609b83166bc323", "src": "hda", "uuid": "f8087fb8-40c8-47b1-990b-78214559261f"}, "sc|soloCBwhitelist": {"id": "b21fb1344711fb0c", "src": "hda", "uuid": "e8684a93-d655-47a1-b18c-efd08b9430bc"}}, "outputs": {"output_log": {"id": "f6cb83298669dabc", "src": "hda", "uuid": "6616cc74-b3eb-46a2-8cfd-9ee8d5efb163"}, "output_genes_filtered": {"id": "c07355fcd885f3e5", "src": "hda", "uuid": "c0be928d-6bcb-41f6-9bb4-50aa98f15c01"}, "output_barcodes_filtered": {"id": "8b10689ed5d7ab17", "src": "hda", "uuid": "78755bd6-46f4-42a8-aa92-c8731c44df85"}, "output_matrix_filtered": {"id": "c6ad493be844d99a", "src": "hda", "uuid": "f35b70c0-d10d-4348-b6fd-1a6d950d255e"}, "output_BAM": {"id": "a405013a715102da", "src": "hda", "uuid": "1264b47e-05c5-41a1-813c-d9e6c6cdfba8"}, "output_stats": {"id": "1a48a8a5831e526a", "src": "hda", "uuid": "86590e09-5319-457c-bc48-4ed0f8dc3831"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Sep 23 07:30:11 ..... started STAR run\nSep 23 07:30:11 ... starting to generate Genome files\nSep 23 07:30:11 ..... processing annotations GTF\nSep 23 07:30:11 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:30:11 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:30:11 ... loading chunks from disk, packing SA...\nSep 23 07:30:11 ... finished generating suffix array\nSep 23 07:30:11 ... generating Suffix Array index\nSep 23 07:30:11 ... completed Suffix Array index\nSep 23 07:30:11 ..... inserting junctions into the genome indices\nSep 23 07:30:11 ... writing Genome to disk ...\nSep 23 07:30:11 ... writing Suffix Array to disk ...\nSep 23 07:30:11 ... writing SAindex to disk\nSep 23 07:30:11 ..... finished successfully\nSep 23 07:30:11 ..... started STAR run\nSep 23 07:30:11 ..... loading genome\nSep 23 07:30:11 ..... started mapping\nSep 23 07:30:29 ..... finished mapping\nSep 23 07:30:29 ..... started Solo counting\nSep 23 07:30:29 ..... finished Solo counting\nSep 23 07:30:29 ..... finished successfully\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Sep 23 07:30:11 ..... started STAR run\nSep 23 07:30:11 ... starting to generate Genome files\nSep 23 07:30:11 ..... processing annotations GTF\nSep 23 07:30:11 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:30:11 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:30:11 ... loading chunks from disk, packing SA...\nSep 23 07:30:11 ... finished generating suffix array\nSep 23 07:30:11 ... generating Suffix Array index\nSep 23 07:30:11 ... completed Suffix Array index\nSep 23 07:30:11 ..... inserting junctions into the genome indices\nSep 23 07:30:11 ... writing Genome to disk ...\nSep 23 07:30:11 ... writing Suffix Array to disk ...\nSep 23 07:30:11 ... writing SAindex to disk\nSep 23 07:30:11 ..... finished successfully\nSep 23 07:30:11 ..... started STAR run\nSep 23 07:30:11 ..... loading genome\nSep 23 07:30:11 ..... started mapping\nSep 23 07:30:29 ..... finished mapping\nSep 23 07:30:29 ..... started Solo counting\nSep 23 07:30:29 ..... finished Solo counting\nSep 23 07:30:29 ..... finished successfully\n", "stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "19.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:30:30", "plugin": "core", "name": "end_epoch", "raw_value": "1727076630.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:30:11", "plugin": "core", "name": "start_epoch", "raw_value": "1727076611.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "rna_starsolo/2.7.8a-1", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 1, "time_seconds": 11.940088510513306, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "rna_starsolo/2.7.8a-2", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 2, "time_seconds": 116.97313356399536, "inputs": {"refGenomeSource|genomeFastaFiles": {"src": "hda", "id": "beafbf6022086882"}, "refGenomeSource|genomeSAindexNbases": "4", "refGenomeSource|sjdbGTFfile": {"src": "hda", "id": "d319d397f5fd926e"}, "refGenomeSource|sjdbOverhang": "100", "refGenomeSource|geneSource": "history", "sc|input_types|input1": [{"src": "hda", "id": "0b3a41832b608f87"}, {"src": "hda", "id": "0b3a41832b608f87"}, {"src": "hda", "id": "0b3a41832b608f87"}], "sc|input_types|input2": [{"src": "hda", "id": "36cfc8b2bc4633ef"}, {"src": "hda", "id": "36cfc8b2bc4633ef"}, {"src": "hda", "id": "36cfc8b2bc4633ef"}], "sc|input_types|use": "repeat", "sc|soloCBwhitelist": {"src": "hda", "id": "4fbb27f2f7287fab"}, "sc|params|chemistry": "CR3", "sc|soloUMIdedup": "1MM_All", "sc|solo_type": "CB_UMI_Simple", "solo|soloStrand": "Forward", "solo|soloFeatures": "Gene"}, "job": {"model_class": "Job", "id": "fd877d819abcee48", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:31:20.344300", "update_time": "2024-09-23T07:32:39.952952", "galaxy_version": "24.1", "external_id": "gxy-hwxvd", "handler": null, "job_runner_name": null, "command_line": "mkdir -p tempstargenomedir && STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' --genomeFastaFiles '/galaxy/server/database/objects/d/8/c/dataset_d8ce4cee-83df-4f50-ace1-5fc290bb70c2.dat' --sjdbOverhang '100' --sjdbGTFfile '/galaxy/server/database/objects/6/3/0/dataset_630e3331-d4d1-4073-906e-82880c7cf57c.dat' --genomeSAindexNbases 4 --runThreadN ${GALAXY_SLOTS:-4} && STAR --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --soloType CB_UMI_Simple --readFilesIn /galaxy/server/database/objects/3/3/6/dataset_33697deb-5b2e-493d-bf2b-aa65fd91dfc9.dat,/galaxy/server/database/objects/3/3/6/dataset_33697deb-5b2e-493d-bf2b-aa65fd91dfc9.dat,/galaxy/server/database/objects/3/3/6/dataset_33697deb-5b2e-493d-bf2b-aa65fd91dfc9.dat /galaxy/server/database/objects/b/9/1/dataset_b91badd8-bd20-4774-b08a-6d2d7d4dab8d.dat,/galaxy/server/database/objects/b/9/1/dataset_b91badd8-bd20-4774-b08a-6d2d7d4dab8d.dat,/galaxy/server/database/objects/b/9/1/dataset_b91badd8-bd20-4774-b08a-6d2d7d4dab8d.dat --soloCBmatchWLtype 1MM_multi --readFilesCommand zcat --soloCBwhitelist '/galaxy/server/database/objects/4/c/1/dataset_4c146d34-8890-4d06-842e-c2fd5081c326.dat' --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloUMIfiltering - --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_All --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --soloCellFilter CellRanger2.2 3000 0.99 10.0 --soloOutFormatFeaturesGeneField3 'Gene Expression' && mv Solo.out/Gene Solo.out/soloFeatures && cat <(echo \"Barcodes:\") Solo.out/Barcodes.stats <(echo \"Genes:\") Solo.out/soloFeatures/Features.stats > '/galaxy/server/database/objects/c/c/9/dataset_cc915879-e7f3-493e-a779-c61c38d1810f.dat' && addthreads=${GALAXY_SLOTS:-2} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/d/d/7/dataset_dd72350f-40a9-4b9c-bf49-2d8d89a27db7.dat' Aligned.out.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "solo": "{\"filter\": {\"__current_case__\": 0, \"filter_type\": \"cellranger2\", \"max_min_ratio\": \"10.0\", \"max_perc\": \"0.99\", \"n_expected\": \"3000\"}, \"soloFeatures\": \"Gene\", \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"soloStrand\": \"Forward\", \"soloUMIfiltering\": \"-\"}", "sc": "{\"__current_case__\": 0, \"input_types\": {\"__current_case__\": 0, \"input1\": {\"values\": [{\"id\": 332, \"src\": \"hda\"}, {\"id\": 332, \"src\": \"hda\"}, {\"id\": 332, \"src\": \"hda\"}]}, \"input2\": {\"values\": [{\"id\": 333, \"src\": \"hda\"}, {\"id\": 333, \"src\": \"hda\"}, {\"id\": 333, \"src\": \"hda\"}]}, \"use\": \"repeat\"}, \"params\": {\"__current_case__\": 1, \"chemistry\": \"CR3\"}, \"soloBarcodeReadLength\": true, \"soloCBmatchWLtype\": \"1MM_multi\", \"soloCBwhitelist\": {\"values\": [{\"id\": 334, \"src\": \"hda\"}]}, \"soloUMIdedup\": \"1MM_All\", \"solo_type\": \"CB_UMI_Simple\"}", "refGenomeSource": "{\"__current_case__\": 1, \"geneSource\": \"history\", \"genomeFastaFiles\": {\"values\": [{\"id\": 335, \"src\": \"hda\"}]}, \"genomeSAindexNbases\": \"4\", \"sjdbGTFfile\": {\"values\": [{\"id\": 331, \"src\": \"hda\"}]}, \"sjdbOverhang\": \"100\"}"}, "inputs": {"sc|input_types|input13": {"id": "0b3a41832b608f87", "src": "hda", "uuid": "b91badd8-bd20-4774-b08a-6d2d7d4dab8d"}, "sc|input_types|input12": {"id": "0b3a41832b608f87", "src": "hda", "uuid": "b91badd8-bd20-4774-b08a-6d2d7d4dab8d"}, "sc|input_types|input11": {"id": "0b3a41832b608f87", "src": "hda", "uuid": "b91badd8-bd20-4774-b08a-6d2d7d4dab8d"}, "sc|input_types|input1": {"id": "0b3a41832b608f87", "src": "hda", "uuid": "b91badd8-bd20-4774-b08a-6d2d7d4dab8d"}, "refGenomeSource|sjdbGTFfile": {"id": "d319d397f5fd926e", "src": "hda", "uuid": "630e3331-d4d1-4073-906e-82880c7cf57c"}, "sc|input_types|input23": {"id": "36cfc8b2bc4633ef", "src": "hda", "uuid": "33697deb-5b2e-493d-bf2b-aa65fd91dfc9"}, "sc|input_types|input22": {"id": "36cfc8b2bc4633ef", "src": "hda", "uuid": "33697deb-5b2e-493d-bf2b-aa65fd91dfc9"}, "sc|input_types|input21": {"id": "36cfc8b2bc4633ef", "src": "hda", "uuid": "33697deb-5b2e-493d-bf2b-aa65fd91dfc9"}, "sc|input_types|input2": {"id": "36cfc8b2bc4633ef", "src": "hda", "uuid": "33697deb-5b2e-493d-bf2b-aa65fd91dfc9"}, "sc|soloCBwhitelist": {"id": "4fbb27f2f7287fab", "src": "hda", "uuid": "4c146d34-8890-4d06-842e-c2fd5081c326"}, "refGenomeSource|genomeFastaFiles": {"id": "e7878fa862de1f40", "src": "hda", "uuid": "d8ce4cee-83df-4f50-ace1-5fc290bb70c2"}}, "outputs": {"output_log": {"id": "eedfaac967aa3c8e", "src": "hda", "uuid": "10711045-adea-4119-81d5-649690ce9799"}, "output_genes_filtered": {"id": "76878f1130db8d78", "src": "hda", "uuid": "0ce721fb-4ddb-40f2-9134-02cf527b89c9"}, "output_barcodes_filtered": {"id": "e7d4b1963f7ed440", "src": "hda", "uuid": "400e4b23-913f-467b-9e2e-5dfd379001a2"}, "output_matrix_filtered": {"id": "3ddf6ace9d044ec5", "src": "hda", "uuid": "25de9058-de17-40a3-b5ba-6868078a0102"}, "output_BAM": {"id": "a1514bea0e3dd162", "src": "hda", "uuid": "dd72350f-40a9-4b9c-bf49-2d8d89a27db7"}, "output_stats": {"id": "6cc7275a431bf448", "src": "hda", "uuid": "cc915879-e7f3-493e-a779-c61c38d1810f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Sep 23 07:31:35 ..... started STAR run\nSep 23 07:31:35 ... starting to generate Genome files\nSep 23 07:31:35 ..... processing annotations GTF\nSep 23 07:31:36 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:31:36 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:31:36 ... loading chunks from disk, packing SA...\nSep 23 07:31:36 ... finished generating suffix array\nSep 23 07:31:36 ... generating Suffix Array index\nSep 23 07:31:36 ... completed Suffix Array index\nSep 23 07:31:36 ..... inserting junctions into the genome indices\nSep 23 07:31:36 ... writing Genome to disk ...\nSep 23 07:31:36 ... writing Suffix Array to disk ...\nSep 23 07:31:36 ... writing SAindex to disk\nSep 23 07:31:36 ..... finished successfully\nSep 23 07:31:36 ..... started STAR run\nSep 23 07:31:36 ..... loading genome\nSep 23 07:31:36 ..... started mapping\nSep 23 07:32:28 ..... finished mapping\nSep 23 07:32:28 ..... started Solo counting\nSep 23 07:32:29 ..... finished Solo counting\nSep 23 07:32:29 ..... finished successfully\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Sep 23 07:31:35 ..... started STAR run\nSep 23 07:31:35 ... starting to generate Genome files\nSep 23 07:31:35 ..... processing annotations GTF\nSep 23 07:31:36 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:31:36 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:31:36 ... loading chunks from disk, packing SA...\nSep 23 07:31:36 ... finished generating suffix array\nSep 23 07:31:36 ... generating Suffix Array index\nSep 23 07:31:36 ... completed Suffix Array index\nSep 23 07:31:36 ..... inserting junctions into the genome indices\nSep 23 07:31:36 ... writing Genome to disk ...\nSep 23 07:31:36 ... writing Suffix Array to disk ...\nSep 23 07:31:36 ... writing SAindex to disk\nSep 23 07:31:36 ..... finished successfully\nSep 23 07:31:36 ..... started STAR run\nSep 23 07:31:36 ..... loading genome\nSep 23 07:31:36 ..... started mapping\nSep 23 07:32:28 ..... finished mapping\nSep 23 07:32:28 ..... started Solo counting\nSep 23 07:32:29 ..... finished Solo counting\nSep 23 07:32:29 ..... finished successfully\n", "stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "54 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "54.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:32:29", "plugin": "core", "name": "end_epoch", "raw_value": "1727076749.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:31:35", "plugin": "core", "name": "start_epoch", "raw_value": "1727076695.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "rna_starsolo/2.7.8a-2", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 2, "time_seconds": 27.311975240707397, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "rna_starsolo/2.7.8a-3", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 3, "time_seconds": 30.227131843566895, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "rna_starsolo/2.7.8a-3", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 3, "time_seconds": 82.57218027114868, "inputs": {"refGenomeSource|genomeFastaFiles": {"src": "hda", "id": "554b4bbc54bfaf13"}, "refGenomeSource|genomeSAindexNbases": "4", "refGenomeSource|sjdbGTFfile": {"src": "hda", "id": "9f5d03b11b0a4e31"}, "refGenomeSource|sjdbOverhang": "100", "refGenomeSource|geneSource": "history", "sc|input_types|input_collection": {"src": "hdca", "id": "b2b30bea50c85ec5"}, "sc|input_types|use": "list_paired", "sc|soloCBwhitelist": {"src": "hda", "id": "b52c43a0e22ca8b7"}, "sc|params|chemistry": "CR3", "sc|soloUMIdedup": "1MM_All", "sc|solo_type": "CB_UMI_Simple", "solo|soloStrand": "Forward", "solo|soloFeatures": "Gene"}, "job": {"model_class": "Job", "id": "eedfaac967aa3c8e", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:40:16.168588", "update_time": "2024-09-23T07:41:00.781969", "galaxy_version": "24.1", "external_id": "gxy-lhhtr", "handler": null, "job_runner_name": null, "command_line": "mkdir -p tempstargenomedir && STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' --genomeFastaFiles '/galaxy/server/database/objects/8/4/e/dataset_84e44051-f2d3-4c87-a357-5510022b75ca.dat' --sjdbOverhang '100' --sjdbGTFfile '/galaxy/server/database/objects/1/7/9/dataset_17954db4-dc6f-40d2-81f3-7f6417adf9bf.dat' --genomeSAindexNbases 4 --runThreadN ${GALAXY_SLOTS:-4} && STAR --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --soloType CB_UMI_Simple --readFilesIn /galaxy/server/database/objects/1/b/8/dataset_1b8f2294-7bd6-42ab-8dc7-18747deea089.dat /galaxy/server/database/objects/a/a/8/dataset_aa89afa1-f1cc-4e20-85c4-e513333af019.dat --soloCBmatchWLtype 1MM_multi --readFilesCommand zcat --soloCBwhitelist '/galaxy/server/database/objects/3/3/a/dataset_33a70441-9d99-4552-9d29-47ead033ec0e.dat' --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloUMIfiltering - --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_All --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --soloCellFilter CellRanger2.2 3000 0.99 10.0 --soloOutFormatFeaturesGeneField3 'Gene Expression' && mv Solo.out/Gene Solo.out/soloFeatures && cat <(echo \"Barcodes:\") Solo.out/Barcodes.stats <(echo \"Genes:\") Solo.out/soloFeatures/Features.stats > '/galaxy/server/database/objects/9/b/a/dataset_9ba45dc3-1dbf-45f7-b8ef-ca0b519a2563.dat' && addthreads=${GALAXY_SLOTS:-2} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/5/5/f/dataset_55f5ea81-1306-4c00-8145-d6cebdb78b98.dat' Aligned.out.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "solo": "{\"filter\": {\"__current_case__\": 0, \"filter_type\": \"cellranger2\", \"max_min_ratio\": \"10.0\", \"max_perc\": \"0.99\", \"n_expected\": \"3000\"}, \"soloFeatures\": \"Gene\", \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"soloStrand\": \"Forward\", \"soloUMIfiltering\": \"-\"}", "sc": "{\"__current_case__\": 0, \"input_types\": {\"__current_case__\": 1, \"input_collection\": {\"values\": [{\"id\": 18, \"src\": \"hdca\"}]}, \"use\": \"list_paired\"}, \"params\": {\"__current_case__\": 1, \"chemistry\": \"CR3\"}, \"soloBarcodeReadLength\": true, \"soloCBmatchWLtype\": \"1MM_multi\", \"soloCBwhitelist\": {\"values\": [{\"id\": 424, \"src\": \"hda\"}]}, \"soloUMIdedup\": \"1MM_All\", \"solo_type\": \"CB_UMI_Simple\"}", "refGenomeSource": "{\"__current_case__\": 1, \"geneSource\": \"history\", \"genomeFastaFiles\": {\"values\": [{\"id\": 425, \"src\": \"hda\"}]}, \"genomeSAindexNbases\": \"4\", \"sjdbGTFfile\": {\"values\": [{\"id\": 421, \"src\": \"hda\"}]}, \"sjdbOverhang\": \"100\"}"}, "inputs": {"refGenomeSource|genomeFastaFiles": {"id": "3806dfc09726926f", "src": "hda", "uuid": "84e44051-f2d3-4c87-a357-5510022b75ca"}, "refGenomeSource|sjdbGTFfile": {"id": "9f5d03b11b0a4e31", "src": "hda", "uuid": "17954db4-dc6f-40d2-81f3-7f6417adf9bf"}, "sc|input_types|input_collection1": {"id": "cf344c6fe2b6ac74", "src": "hda", "uuid": "aa89afa1-f1cc-4e20-85c4-e513333af019"}, "sc|input_types|input_collection2": {"id": "b3a11f08b11e805f", "src": "hda", "uuid": "1b8f2294-7bd6-42ab-8dc7-18747deea089"}, "sc|soloCBwhitelist": {"id": "b52c43a0e22ca8b7", "src": "hda", "uuid": "33a70441-9d99-4552-9d29-47ead033ec0e"}}, "outputs": {"output_stats": {"id": "0308a5f7176b3907", "src": "hda", "uuid": "9ba45dc3-1dbf-45f7-b8ef-ca0b519a2563"}, "output_BAM": {"id": "73eb8b424f6567ff", "src": "hda", "uuid": "55f5ea81-1306-4c00-8145-d6cebdb78b98"}, "output_matrix_filtered": {"id": "3794a20af6d34e2d", "src": "hda", "uuid": "b1982088-a4d8-4667-81ee-871b103faa17"}, "output_barcodes_filtered": {"id": "e3c6a31a02615b26", "src": "hda", "uuid": "a44aa46f-b7cb-4139-a9fc-1778ade83e8d"}, "output_genes_filtered": {"id": "40f9c51263393d0f", "src": "hda", "uuid": "6f7853ac-e468-4ae0-9efb-a2f7a4f55071"}, "output_log": {"id": "e3c137aa75bd2edf", "src": "hda", "uuid": "0e24b258-2c77-4451-a4bd-109354751577"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Sep 23 07:40:30 ..... started STAR run\nSep 23 07:40:30 ... starting to generate Genome files\nSep 23 07:40:30 ..... processing annotations GTF\nSep 23 07:40:30 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:40:30 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:40:31 ... loading chunks from disk, packing SA...\nSep 23 07:40:31 ... finished generating suffix array\nSep 23 07:40:31 ... generating Suffix Array index\nSep 23 07:40:31 ... completed Suffix Array index\nSep 23 07:40:31 ..... inserting junctions into the genome indices\nSep 23 07:40:31 ... writing Genome to disk ...\nSep 23 07:40:31 ... writing Suffix Array to disk ...\nSep 23 07:40:31 ... writing SAindex to disk\nSep 23 07:40:31 ..... finished successfully\nSep 23 07:40:31 ..... started STAR run\nSep 23 07:40:31 ..... loading genome\nSep 23 07:40:31 ..... started mapping\nSep 23 07:40:49 ..... finished mapping\nSep 23 07:40:49 ..... started Solo counting\nSep 23 07:40:49 ..... finished Solo counting\nSep 23 07:40:49 ..... finished successfully\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Sep 23 07:40:30 ..... started STAR run\nSep 23 07:40:30 ... starting to generate Genome files\nSep 23 07:40:30 ..... processing annotations GTF\nSep 23 07:40:30 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:40:30 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:40:31 ... loading chunks from disk, packing SA...\nSep 23 07:40:31 ... finished generating suffix array\nSep 23 07:40:31 ... generating Suffix Array index\nSep 23 07:40:31 ... completed Suffix Array index\nSep 23 07:40:31 ..... inserting junctions into the genome indices\nSep 23 07:40:31 ... writing Genome to disk ...\nSep 23 07:40:31 ... writing Suffix Array to disk ...\nSep 23 07:40:31 ... writing SAindex to disk\nSep 23 07:40:31 ..... finished successfully\nSep 23 07:40:31 ..... started STAR run\nSep 23 07:40:31 ..... loading genome\nSep 23 07:40:31 ..... started mapping\nSep 23 07:40:49 ..... finished mapping\nSep 23 07:40:49 ..... started Solo counting\nSep 23 07:40:49 ..... finished Solo counting\nSep 23 07:40:49 ..... finished successfully\n", "stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "19.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:40:49", "plugin": "core", "name": "end_epoch", "raw_value": "1727077249.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:40:30", "plugin": "core", "name": "start_epoch", "raw_value": "1727077230.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "rna_starsolo/2.7.8a-4", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 4, "time_seconds": 12.524164915084839, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "rna_starsolo/2.7.8a-4", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 4, "time_seconds": 81.81027245521545, "inputs": {"refGenomeSource|genomeFastaFiles": {"src": "hda", "id": "ab46a99db69375ce"}, "refGenomeSource|genomeSAindexNbases": "4", "refGenomeSource|sjdbGTFfile": {"src": "hda", "id": "363809241d2e2d64"}, "refGenomeSource|sjdbOverhang": "100", "refGenomeSource|geneSource": "history", "sc|input_types|input1": {"src": "hda", "id": "d9aac45ce2572489"}, "sc|input_types|input2": {"src": "hda", "id": "3a43f49bacecc110"}, "sc|input_types|use": "repeat", "sc|soloCBwhitelist": {"src": "hda", "id": "1a49bfec6f972a4d"}, "sc|params|chemistry": "CR3", "sc|soloUMIdedup": "1MM_All", "sc|soloCBmatchWLtype": "1MM_multi_pseudocounts", "sc|solo_type": "CB_UMI_Simple", "solo|soloStrand": "Forward", "solo|soloFeatures": "GeneFull", "solo|soloUMIfiltering": "MultiGeneUMI", "solo|filter|n_cells": "5", "solo|filter|filter_type": "topcells", "solo|soloOutFormatFeaturesGeneField3": "Dummy Text"}, "job": {"model_class": "Job", "id": "209a69703347edde", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:41:37.484904", "update_time": "2024-09-23T07:42:22.550171", "galaxy_version": "24.1", "external_id": "gxy-xk2tp", "handler": null, "job_runner_name": null, "command_line": "mkdir -p tempstargenomedir && STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' --genomeFastaFiles '/galaxy/server/database/objects/1/e/2/dataset_1e2e5712-332e-4646-b9e9-5ac651117e7e.dat' --sjdbOverhang '100' --sjdbGTFfile '/galaxy/server/database/objects/e/0/a/dataset_e0afd8d5-b571-480b-98da-6a2fffcf7f9a.dat' --genomeSAindexNbases 4 --runThreadN ${GALAXY_SLOTS:-4} && STAR --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --soloType CB_UMI_Simple --readFilesIn /galaxy/server/database/objects/7/1/8/dataset_718abb21-99fe-4b23-83b4-af99dd92beb8.dat /galaxy/server/database/objects/4/f/7/dataset_4f7ab695-e6c9-48e1-b54f-45bc213b2461.dat --soloCBmatchWLtype 1MM_multi_pseudocounts --readFilesCommand zcat --soloCBwhitelist '/galaxy/server/database/objects/f/0/d/dataset_f0de9b9f-182e-434a-97e7-4475a8b74d59.dat' --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloUMIfiltering MultiGeneUMI --soloStrand Forward --soloFeatures GeneFull --soloUMIdedup 1MM_All --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --soloCellFilter TopCells 5 --soloOutFormatFeaturesGeneField3 'Dummy Text' && mv Solo.out/GeneFull Solo.out/soloFeatures && cat <(echo \"Barcodes:\") Solo.out/Barcodes.stats <(echo \"Genes:\") Solo.out/soloFeatures/Features.stats > '/galaxy/server/database/objects/5/9/e/dataset_59e5c66b-ef65-467e-9295-7f8cb70a8d33.dat' && addthreads=${GALAXY_SLOTS:-2} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/7/9/9/dataset_79905383-e2a4-42b1-b9f7-021d34ad3331.dat' Aligned.out.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "solo": "{\"filter\": {\"__current_case__\": 2, \"filter_type\": \"topcells\", \"n_cells\": \"5\"}, \"soloFeatures\": \"GeneFull\", \"soloOutFormatFeaturesGeneField3\": \"Dummy Text\", \"soloStrand\": \"Forward\", \"soloUMIfiltering\": \"MultiGeneUMI\"}", "sc": "{\"__current_case__\": 0, \"input_types\": {\"__current_case__\": 0, \"input1\": {\"values\": [{\"id\": 434, \"src\": \"hda\"}]}, \"input2\": {\"values\": [{\"id\": 435, \"src\": \"hda\"}]}, \"use\": \"repeat\"}, \"params\": {\"__current_case__\": 1, \"chemistry\": \"CR3\"}, \"soloBarcodeReadLength\": true, \"soloCBmatchWLtype\": \"1MM_multi_pseudocounts\", \"soloCBwhitelist\": {\"values\": [{\"id\": 436, \"src\": \"hda\"}]}, \"soloUMIdedup\": \"1MM_All\", \"solo_type\": \"CB_UMI_Simple\"}", "refGenomeSource": "{\"__current_case__\": 1, \"geneSource\": \"history\", \"genomeFastaFiles\": {\"values\": [{\"id\": 437, \"src\": \"hda\"}]}, \"genomeSAindexNbases\": \"4\", \"sjdbGTFfile\": {\"values\": [{\"id\": 433, \"src\": \"hda\"}]}, \"sjdbOverhang\": \"100\"}"}, "inputs": {"refGenomeSource|genomeFastaFiles": {"id": "22e54f81ccf8e76d", "src": "hda", "uuid": "1e2e5712-332e-4646-b9e9-5ac651117e7e"}, "refGenomeSource|sjdbGTFfile": {"id": "363809241d2e2d64", "src": "hda", "uuid": "e0afd8d5-b571-480b-98da-6a2fffcf7f9a"}, "sc|input_types|input1": {"id": "d9aac45ce2572489", "src": "hda", "uuid": "4f7ab695-e6c9-48e1-b54f-45bc213b2461"}, "sc|input_types|input11": {"id": "d9aac45ce2572489", "src": "hda", "uuid": "4f7ab695-e6c9-48e1-b54f-45bc213b2461"}, "sc|input_types|input2": {"id": "3a43f49bacecc110", "src": "hda", "uuid": "718abb21-99fe-4b23-83b4-af99dd92beb8"}, "sc|input_types|input21": {"id": "3a43f49bacecc110", "src": "hda", "uuid": "718abb21-99fe-4b23-83b4-af99dd92beb8"}, "sc|soloCBwhitelist": {"id": "1a49bfec6f972a4d", "src": "hda", "uuid": "f0de9b9f-182e-434a-97e7-4475a8b74d59"}}, "outputs": {"output_stats": {"id": "12fa808178409019", "src": "hda", "uuid": "59e5c66b-ef65-467e-9295-7f8cb70a8d33"}, "output_BAM": {"id": "d8431777c8df900c", "src": "hda", "uuid": "79905383-e2a4-42b1-b9f7-021d34ad3331"}, "output_matrixGeneFull_filtered": {"id": "f477e68de21aded7", "src": "hda", "uuid": "77bdedad-454c-4ad5-ad1c-9d34e7fa50e8"}, "output_barcodes_filtered": {"id": "f23cf37eb18611a1", "src": "hda", "uuid": "c5f1d83d-2214-4b30-a7b9-df08efa87325"}, "output_genes_filtered": {"id": "97262d7a3c1436b0", "src": "hda", "uuid": "ae6ab404-c70c-4c80-a1c4-e374be4e9b3f"}, "output_log": {"id": "63202692711a29c2", "src": "hda", "uuid": "5c8c46c1-f472-4e4f-8e92-149e34f75d96"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Sep 23 07:41:52 ..... started STAR run\nSep 23 07:41:52 ... starting to generate Genome files\nSep 23 07:41:52 ..... processing annotations GTF\nSep 23 07:41:52 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:41:52 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:41:52 ... loading chunks from disk, packing SA...\nSep 23 07:41:52 ... finished generating suffix array\nSep 23 07:41:52 ... generating Suffix Array index\nSep 23 07:41:52 ... completed Suffix Array index\nSep 23 07:41:52 ..... inserting junctions into the genome indices\nSep 23 07:41:52 ... writing Genome to disk ...\nSep 23 07:41:52 ... writing Suffix Array to disk ...\nSep 23 07:41:52 ... writing SAindex to disk\nSep 23 07:41:52 ..... finished successfully\nSep 23 07:41:52 ..... started STAR run\nSep 23 07:41:52 ..... loading genome\nSep 23 07:41:52 ..... started mapping\nSep 23 07:42:10 ..... finished mapping\nSep 23 07:42:10 ..... started Solo counting\nSep 23 07:42:10 ..... finished Solo counting\nSep 23 07:42:10 ..... finished successfully\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Sep 23 07:41:52 ..... started STAR run\nSep 23 07:41:52 ... starting to generate Genome files\nSep 23 07:41:52 ..... processing annotations GTF\nSep 23 07:41:52 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:41:52 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:41:52 ... loading chunks from disk, packing SA...\nSep 23 07:41:52 ... finished generating suffix array\nSep 23 07:41:52 ... generating Suffix Array index\nSep 23 07:41:52 ... completed Suffix Array index\nSep 23 07:41:52 ..... inserting junctions into the genome indices\nSep 23 07:41:52 ... writing Genome to disk ...\nSep 23 07:41:52 ... writing Suffix Array to disk ...\nSep 23 07:41:52 ... writing SAindex to disk\nSep 23 07:41:52 ..... finished successfully\nSep 23 07:41:52 ..... started STAR run\nSep 23 07:41:52 ..... loading genome\nSep 23 07:41:52 ..... started mapping\nSep 23 07:42:10 ..... finished mapping\nSep 23 07:42:10 ..... started Solo counting\nSep 23 07:42:10 ..... finished Solo counting\nSep 23 07:42:10 ..... finished successfully\n", "stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "19.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:42:11", "plugin": "core", "name": "end_epoch", "raw_value": "1727077331.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:41:52", "plugin": "core", "name": "start_epoch", "raw_value": "1727077312.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "rna_starsolo/2.7.8a-5", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 5, "time_seconds": 85.26931643486023, "inputs": {"refGenomeSource|genomeFastaFiles": {"src": "hda", "id": "e3e7a4141b23f3d4"}, "refGenomeSource|genomeSAindexNbases": "4", "refGenomeSource|sjdbGTFfile": {"src": "hda", "id": "7ace0f4c6d1e0d3b"}, "refGenomeSource|sjdbOverhang": "100", "refGenomeSource|geneSource": "history", "sc|input_types|input1": {"src": "hda", "id": "5e8a6a519aaa54ad"}, "sc|input_types|input2": {"src": "hda", "id": "c77a9fa897ef20a0"}, "sc|input_types|use": "repeat", "sc|soloCBwhitelist": {"src": "hda", "id": "c5dd26505d988ac8"}, "sc|params|chemistry": "CR3", "sc|soloUMIdedup": "1MM_All", "sc|solo_type": "CB_UMI_Simple", "solo|soloStrand": "Forward", "solo|soloFeatures": "Gene", "solo|filter|nExpectedCells": "5", "solo|filter|maxPercentile": "0.99", "solo|filter|maxMinRatio": "10", "solo|filter|indMin": "45000", "solo|filter|indMax": "90000", "solo|filter|umiMin": "500", "solo|filter|umiMinFracMedian": "0.01", "solo|filter|candMaxN": "20000", "solo|filter|FDR": "0.01", "solo|filter|simN": "10000", "solo|filter|filter_type": "emptydrops"}, "job": {"model_class": "Job", "id": "bdc88e9437af602c", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:34:02.528764", "update_time": "2024-09-23T07:34:46.853613", "galaxy_version": "24.1", "external_id": "gxy-b26dt", "handler": null, "job_runner_name": null, "command_line": "mkdir -p tempstargenomedir && STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' --genomeFastaFiles '/galaxy/server/database/objects/9/c/5/dataset_9c5ac04d-d692-4e38-87f6-c4d54c04e84b.dat' --sjdbOverhang '100' --sjdbGTFfile '/galaxy/server/database/objects/c/9/2/dataset_c9231d46-2322-4e74-97d3-5a755999c417.dat' --genomeSAindexNbases 4 --runThreadN ${GALAXY_SLOTS:-4} && STAR --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --soloType CB_UMI_Simple --readFilesIn /galaxy/server/database/objects/f/5/b/dataset_f5b71207-bc69-4209-800d-4e227180f7dd.dat /galaxy/server/database/objects/1/e/3/dataset_1e3ef30b-5276-4fce-8e21-21c783699e0f.dat --soloCBmatchWLtype 1MM_multi --readFilesCommand zcat --soloCBwhitelist '/galaxy/server/database/objects/0/9/c/dataset_09c155a3-af37-4c91-a754-4f514b9d3e26.dat' --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloUMIfiltering - --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_All --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --soloCellFilter EmptyDrops_CR 5 0.99 10.0 45000 90000 500 0.01 20000 0.01 10000 --soloOutFormatFeaturesGeneField3 'Gene Expression' && mv Solo.out/Gene Solo.out/soloFeatures && cat <(echo \"Barcodes:\") Solo.out/Barcodes.stats <(echo \"Genes:\") Solo.out/soloFeatures/Features.stats > '/galaxy/server/database/objects/1/b/d/dataset_1bd09d94-3d68-48ac-b03f-ea20066c13e3.dat' && addthreads=${GALAXY_SLOTS:-2} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/9/2/8/dataset_92832c02-bdfe-484c-956a-09368066ecdf.dat' Aligned.out.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "solo": "{\"filter\": {\"FDR\": \"0.01\", \"__current_case__\": 1, \"candMaxN\": \"20000\", \"filter_type\": \"emptydrops\", \"indMax\": \"90000\", \"indMin\": \"45000\", \"maxMinRatio\": \"10.0\", \"maxPercentile\": \"0.99\", \"nExpectedCells\": \"5\", \"simN\": \"10000\", \"umiMin\": \"500\", \"umiMinFracMedian\": \"0.01\"}, \"soloFeatures\": \"Gene\", \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"soloStrand\": \"Forward\", \"soloUMIfiltering\": \"-\"}", "sc": "{\"__current_case__\": 0, \"input_types\": {\"__current_case__\": 0, \"input1\": {\"values\": [{\"id\": 354, \"src\": \"hda\"}]}, \"input2\": {\"values\": [{\"id\": 355, \"src\": \"hda\"}]}, \"use\": \"repeat\"}, \"params\": {\"__current_case__\": 1, \"chemistry\": \"CR3\"}, \"soloBarcodeReadLength\": true, \"soloCBmatchWLtype\": \"1MM_multi\", \"soloCBwhitelist\": {\"values\": [{\"id\": 356, \"src\": \"hda\"}]}, \"soloUMIdedup\": \"1MM_All\", \"solo_type\": \"CB_UMI_Simple\"}", "refGenomeSource": "{\"__current_case__\": 1, \"geneSource\": \"history\", \"genomeFastaFiles\": {\"values\": [{\"id\": 357, \"src\": \"hda\"}]}, \"genomeSAindexNbases\": \"4\", \"sjdbGTFfile\": {\"values\": [{\"id\": 353, \"src\": \"hda\"}]}, \"sjdbOverhang\": \"100\"}"}, "inputs": {"refGenomeSource|genomeFastaFiles": {"id": "4c47b6ca15d06670", "src": "hda", "uuid": "9c5ac04d-d692-4e38-87f6-c4d54c04e84b"}, "refGenomeSource|sjdbGTFfile": {"id": "7ace0f4c6d1e0d3b", "src": "hda", "uuid": "c9231d46-2322-4e74-97d3-5a755999c417"}, "sc|input_types|input1": {"id": "5e8a6a519aaa54ad", "src": "hda", "uuid": "1e3ef30b-5276-4fce-8e21-21c783699e0f"}, "sc|input_types|input11": {"id": "5e8a6a519aaa54ad", "src": "hda", "uuid": "1e3ef30b-5276-4fce-8e21-21c783699e0f"}, "sc|input_types|input2": {"id": "c77a9fa897ef20a0", "src": "hda", "uuid": "f5b71207-bc69-4209-800d-4e227180f7dd"}, "sc|input_types|input21": {"id": "c77a9fa897ef20a0", "src": "hda", "uuid": "f5b71207-bc69-4209-800d-4e227180f7dd"}, "sc|soloCBwhitelist": {"id": "c5dd26505d988ac8", "src": "hda", "uuid": "09c155a3-af37-4c91-a754-4f514b9d3e26"}}, "outputs": {"output_log": {"id": "82eefcb619038931", "src": "hda", "uuid": "b2f46b11-e929-485e-b735-14ae07800f49"}, "output_genes_filtered": {"id": "c6361f39b7bb7603", "src": "hda", "uuid": "59ac4b3a-8c49-460c-bcd1-caf7c6554956"}, "output_barcodes_filtered": {"id": "5d04a2766377a28d", "src": "hda", "uuid": "46fd1c7a-c4a8-429a-9e9f-f17e4668cfb9"}, "output_matrix_filtered": {"id": "f6a4e70feba0927c", "src": "hda", "uuid": "a95ffacb-3adc-4a7f-847a-63a4336aec7c"}, "output_BAM": {"id": "e5c645816530c5e9", "src": "hda", "uuid": "92832c02-bdfe-484c-956a-09368066ecdf"}, "output_stats": {"id": "bdfcd3fbf37e3201", "src": "hda", "uuid": "1bd09d94-3d68-48ac-b03f-ea20066c13e3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Sep 23 07:34:16 ..... started STAR run\nSep 23 07:34:16 ... starting to generate Genome files\nSep 23 07:34:17 ..... processing annotations GTF\nSep 23 07:34:17 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:34:17 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:34:17 ... loading chunks from disk, packing SA...\nSep 23 07:34:17 ... finished generating suffix array\nSep 23 07:34:17 ... generating Suffix Array index\nSep 23 07:34:17 ... completed Suffix Array index\nSep 23 07:34:17 ..... inserting junctions into the genome indices\nSep 23 07:34:17 ... writing Genome to disk ...\nSep 23 07:34:17 ... writing Suffix Array to disk ...\nSep 23 07:34:17 ... writing SAindex to disk\nSep 23 07:34:17 ..... finished successfully\nSep 23 07:34:17 ..... started STAR run\nSep 23 07:34:17 ..... loading genome\nSep 23 07:34:17 ..... started mapping\nSep 23 07:34:35 ..... finished mapping\nSep 23 07:34:35 ..... started Solo counting\nSep 23 07:34:35 ..... finished Solo counting\nSep 23 07:34:35 ..... finished successfully\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Sep 23 07:34:16 ..... started STAR run\nSep 23 07:34:16 ... starting to generate Genome files\nSep 23 07:34:17 ..... processing annotations GTF\nSep 23 07:34:17 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:34:17 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:34:17 ... loading chunks from disk, packing SA...\nSep 23 07:34:17 ... finished generating suffix array\nSep 23 07:34:17 ... generating Suffix Array index\nSep 23 07:34:17 ... completed Suffix Array index\nSep 23 07:34:17 ..... inserting junctions into the genome indices\nSep 23 07:34:17 ... writing Genome to disk ...\nSep 23 07:34:17 ... writing Suffix Array to disk ...\nSep 23 07:34:17 ... writing SAindex to disk\nSep 23 07:34:17 ..... finished successfully\nSep 23 07:34:17 ..... started STAR run\nSep 23 07:34:17 ..... loading genome\nSep 23 07:34:17 ..... started mapping\nSep 23 07:34:35 ..... finished mapping\nSep 23 07:34:35 ..... started Solo counting\nSep 23 07:34:35 ..... finished Solo counting\nSep 23 07:34:35 ..... finished successfully\n", "stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "19.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:34:35", "plugin": "core", "name": "end_epoch", "raw_value": "1727076875.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:34:16", "plugin": "core", "name": "start_epoch", "raw_value": "1727076856.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "rna_starsolo/2.7.8a-5", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 5, "time_seconds": 84.36227750778198, "inputs": {"refGenomeSource|genomeFastaFiles": {"src": "hda", "id": "e901b4616acbf4c6"}, "refGenomeSource|genomeSAindexNbases": "4", "refGenomeSource|sjdbGTFfile": {"src": "hda", "id": "a1ded5dea4d507e6"}, "refGenomeSource|sjdbOverhang": "100", "refGenomeSource|geneSource": "history", "sc|input_types|input1": {"src": "hda", "id": "0adc3bd0aef531f6"}, "sc|input_types|input2": {"src": "hda", "id": "5d8fffa9b5064291"}, "sc|input_types|use": "repeat", "sc|soloCBwhitelist": {"src": "hda", "id": "170e4d34711da88a"}, "sc|params|chemistry": "CR3", "sc|soloUMIdedup": "1MM_All", "sc|solo_type": "CB_UMI_Simple", "solo|soloStrand": "Forward", "solo|soloFeatures": "Gene", "solo|filter|nExpectedCells": "5", "solo|filter|maxPercentile": "0.99", "solo|filter|maxMinRatio": "10", "solo|filter|indMin": "45000", "solo|filter|indMax": "90000", "solo|filter|umiMin": "500", "solo|filter|umiMinFracMedian": "0.01", "solo|filter|candMaxN": "20000", "solo|filter|FDR": "0.01", "solo|filter|simN": "10000", "solo|filter|filter_type": "emptydrops"}, "job": {"model_class": "Job", "id": "c267034d63e0e219", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:43:00.861409", "update_time": "2024-09-23T07:43:46.143068", "galaxy_version": "24.1", "external_id": "gxy-24zjk", "handler": null, "job_runner_name": null, "command_line": "mkdir -p tempstargenomedir && STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' --genomeFastaFiles '/galaxy/server/database/objects/f/4/0/dataset_f40d9907-1c6b-406d-b768-e02343796230.dat' --sjdbOverhang '100' --sjdbGTFfile '/galaxy/server/database/objects/6/e/e/dataset_6ee2e2c3-8970-46da-bce1-c85f6db1a81e.dat' --genomeSAindexNbases 4 --runThreadN ${GALAXY_SLOTS:-4} && STAR --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --soloType CB_UMI_Simple --readFilesIn /galaxy/server/database/objects/8/9/1/dataset_89130849-0e18-44a4-bdc1-dc1a69fb23f1.dat /galaxy/server/database/objects/2/7/6/dataset_276c3a45-e83d-4010-b9c7-bf4770defa4f.dat --soloCBmatchWLtype 1MM_multi --readFilesCommand zcat --soloCBwhitelist '/galaxy/server/database/objects/1/f/2/dataset_1f23957c-bc93-477f-8d2d-b103fbaa9ee5.dat' --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloUMIfiltering - --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_All --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --soloCellFilter EmptyDrops_CR 5 0.99 10.0 45000 90000 500 0.01 20000 0.01 10000 --soloOutFormatFeaturesGeneField3 'Gene Expression' && mv Solo.out/Gene Solo.out/soloFeatures && cat <(echo \"Barcodes:\") Solo.out/Barcodes.stats <(echo \"Genes:\") Solo.out/soloFeatures/Features.stats > '/galaxy/server/database/objects/0/7/7/dataset_0773974d-a900-409d-be61-88530dc1f495.dat' && addthreads=${GALAXY_SLOTS:-2} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/3/a/d/dataset_3ad28f43-5c2a-4aee-9a1d-b6bda94b9d26.dat' Aligned.out.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "solo": "{\"filter\": {\"FDR\": \"0.01\", \"__current_case__\": 1, \"candMaxN\": \"20000\", \"filter_type\": \"emptydrops\", \"indMax\": \"90000\", \"indMin\": \"45000\", \"maxMinRatio\": \"10.0\", \"maxPercentile\": \"0.99\", \"nExpectedCells\": \"5\", \"simN\": \"10000\", \"umiMin\": \"500\", \"umiMinFracMedian\": \"0.01\"}, \"soloFeatures\": \"Gene\", \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"soloStrand\": \"Forward\", \"soloUMIfiltering\": \"-\"}", "sc": "{\"__current_case__\": 0, \"input_types\": {\"__current_case__\": 0, \"input1\": {\"values\": [{\"id\": 446, \"src\": \"hda\"}]}, \"input2\": {\"values\": [{\"id\": 447, \"src\": \"hda\"}]}, \"use\": \"repeat\"}, \"params\": {\"__current_case__\": 1, \"chemistry\": \"CR3\"}, \"soloBarcodeReadLength\": true, \"soloCBmatchWLtype\": \"1MM_multi\", \"soloCBwhitelist\": {\"values\": [{\"id\": 448, \"src\": \"hda\"}]}, \"soloUMIdedup\": \"1MM_All\", \"solo_type\": \"CB_UMI_Simple\"}", "refGenomeSource": "{\"__current_case__\": 1, \"geneSource\": \"history\", \"genomeFastaFiles\": {\"values\": [{\"id\": 449, \"src\": \"hda\"}]}, \"genomeSAindexNbases\": \"4\", \"sjdbGTFfile\": {\"values\": [{\"id\": 445, \"src\": \"hda\"}]}, \"sjdbOverhang\": \"100\"}"}, "inputs": {"refGenomeSource|genomeFastaFiles": {"id": "9a832fbfba85c161", "src": "hda", "uuid": "f40d9907-1c6b-406d-b768-e02343796230"}, "refGenomeSource|sjdbGTFfile": {"id": "a1ded5dea4d507e6", "src": "hda", "uuid": "6ee2e2c3-8970-46da-bce1-c85f6db1a81e"}, "sc|input_types|input1": {"id": "0adc3bd0aef531f6", "src": "hda", "uuid": "276c3a45-e83d-4010-b9c7-bf4770defa4f"}, "sc|input_types|input11": {"id": "0adc3bd0aef531f6", "src": "hda", "uuid": "276c3a45-e83d-4010-b9c7-bf4770defa4f"}, "sc|input_types|input2": {"id": "5d8fffa9b5064291", "src": "hda", "uuid": "89130849-0e18-44a4-bdc1-dc1a69fb23f1"}, "sc|input_types|input21": {"id": "5d8fffa9b5064291", "src": "hda", "uuid": "89130849-0e18-44a4-bdc1-dc1a69fb23f1"}, "sc|soloCBwhitelist": {"id": "170e4d34711da88a", "src": "hda", "uuid": "1f23957c-bc93-477f-8d2d-b103fbaa9ee5"}}, "outputs": {"output_stats": {"id": "6b7c86b97a8ff485", "src": "hda", "uuid": "0773974d-a900-409d-be61-88530dc1f495"}, "output_BAM": {"id": "df5f6abe41a2d309", "src": "hda", "uuid": "3ad28f43-5c2a-4aee-9a1d-b6bda94b9d26"}, "output_matrix_filtered": {"id": "5449d4ad7a1879ff", "src": "hda", "uuid": "39861400-c336-4529-b341-cda4067820c1"}, "output_barcodes_filtered": {"id": "003db7640f949660", "src": "hda", "uuid": "6070c206-b35a-445f-b46d-921cf62e96fc"}, "output_genes_filtered": {"id": "a6cc817bfc3a7cf1", "src": "hda", "uuid": "84c414ee-3df7-4e60-8ff2-3279dc1eda95"}, "output_log": {"id": "698ae6f4926183f9", "src": "hda", "uuid": "e5990ee5-2ea8-40a9-8f1d-ef9ac3656261"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Sep 23 07:43:16 ..... started STAR run\nSep 23 07:43:16 ... starting to generate Genome files\nSep 23 07:43:16 ..... processing annotations GTF\nSep 23 07:43:16 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:43:16 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:43:16 ... loading chunks from disk, packing SA...\nSep 23 07:43:16 ... finished generating suffix array\nSep 23 07:43:16 ... generating Suffix Array index\nSep 23 07:43:16 ... completed Suffix Array index\nSep 23 07:43:16 ..... inserting junctions into the genome indices\nSep 23 07:43:16 ... writing Genome to disk ...\nSep 23 07:43:16 ... writing Suffix Array to disk ...\nSep 23 07:43:16 ... writing SAindex to disk\nSep 23 07:43:16 ..... finished successfully\nSep 23 07:43:16 ..... started STAR run\nSep 23 07:43:16 ..... loading genome\nSep 23 07:43:16 ..... started mapping\nSep 23 07:43:34 ..... finished mapping\nSep 23 07:43:34 ..... started Solo counting\nSep 23 07:43:34 ..... finished Solo counting\nSep 23 07:43:34 ..... finished successfully\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Sep 23 07:43:16 ..... started STAR run\nSep 23 07:43:16 ... starting to generate Genome files\nSep 23 07:43:16 ..... processing annotations GTF\nSep 23 07:43:16 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:43:16 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:43:16 ... loading chunks from disk, packing SA...\nSep 23 07:43:16 ... finished generating suffix array\nSep 23 07:43:16 ... generating Suffix Array index\nSep 23 07:43:16 ... completed Suffix Array index\nSep 23 07:43:16 ..... inserting junctions into the genome indices\nSep 23 07:43:16 ... writing Genome to disk ...\nSep 23 07:43:16 ... writing Suffix Array to disk ...\nSep 23 07:43:16 ... writing SAindex to disk\nSep 23 07:43:16 ..... finished successfully\nSep 23 07:43:16 ..... started STAR run\nSep 23 07:43:16 ..... loading genome\nSep 23 07:43:16 ..... started mapping\nSep 23 07:43:34 ..... finished mapping\nSep 23 07:43:34 ..... started Solo counting\nSep 23 07:43:34 ..... finished Solo counting\nSep 23 07:43:34 ..... finished successfully\n", "stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "18 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "18.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:43:34", "plugin": "core", "name": "end_epoch", "raw_value": "1727077414.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:43:16", "plugin": "core", "name": "start_epoch", "raw_value": "1727077396.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "rna_starsolo/2.7.8a-6", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 6, "time_seconds": 74.5870349407196, "inputs": {"refGenomeSource|genomeFastaFiles": {"src": "hda", "id": "6465231d7923c4e0"}, "refGenomeSource|genomeSAindexNbases": "4", "refGenomeSource|sjdbGTFfile": {"src": "hda", "id": "846ffe24b03641b2"}, "refGenomeSource|sjdbOverhang": "100", "refGenomeSource|geneSource": "history", "sc|input_types|input1": {"src": "hda", "id": "9ff6042cd60b7057"}, "sc|input_types|input2": {"src": "hda", "id": "50ab40971672b37c"}, "sc|input_types|use": "repeat", "sc|cb_whitelists_0|whitelist_file": {"src": "hda", "id": "b6b30d78304c60e5"}, "sc|cb_whitelists_0|cb_start_anchor": "0", "sc|cb_whitelists_0|cb_start_anchor_pos": "0", "sc|cb_whitelists_0|cb_end_anchor": "2", "sc|cb_whitelists_0|cb_end_anchor_pos": "-1", "sc|cb_whitelists_1|whitelist_file": {"src": "hda", "id": "bf62718d3a20ff23"}, "sc|cb_whitelists_1|cb_start_anchor": "3", "sc|cb_whitelists_1|cb_start_anchor_pos": "1", "sc|cb_whitelists_1|cb_end_anchor": "3", "sc|cb_whitelists_1|cb_end_anchor_pos": "8", "sc|umi_start_anchor": "3", "sc|umi_start_anchor_pos": "9", "sc|umi_end_anchor": "3", "sc|umi_end_anchor_pos": "14", "sc|soloAdapterSequence": "GAGTGATTGCTTGTGACGCCTT", "sc|soloAdapterMismatchesNmax": "1", "sc|clipAdapterType": "CellRanger4", "sc|soloUMIdedup": "1MM_All", "sc|soloCBmatchWLtype": "1MM", "sc|solo_type": "CB_UMI_Complex"}, "job": {"model_class": "Job", "id": "6520e1f6478ad976", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:35:32.220220", "update_time": "2024-09-23T07:36:01.871166", "galaxy_version": "24.1", "external_id": "gxy-j8r4c", "handler": null, "job_runner_name": null, "command_line": "mkdir -p tempstargenomedir && STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' --genomeFastaFiles '/galaxy/server/database/objects/4/d/2/dataset_4d2a3aba-6a44-4169-8525-772a46846cee.dat' --sjdbOverhang '100' --sjdbGTFfile '/galaxy/server/database/objects/f/3/8/dataset_f38d8870-e0b7-476b-bf54-c8abfe3b2125.dat' --genomeSAindexNbases 4 --runThreadN ${GALAXY_SLOTS:-4} && STAR --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --soloType CB_UMI_Complex --readFilesIn /galaxy/server/database/objects/f/4/c/dataset_f4cfd952-e970-4021-8a20-33ae6eafa10c.dat /galaxy/server/database/objects/9/f/d/dataset_9fda1f18-2f67-4046-bf7d-e1afc5f02467.dat --soloCBmatchWLtype 1MM --readFilesCommand zcat --soloCBwhitelist /galaxy/server/database/objects/9/0/6/dataset_906ecbf4-fa5e-4c09-9410-bad4028dfe67.dat /galaxy/server/database/objects/8/3/2/dataset_8327c0f3-f5b8-459e-a030-eaef47d4e306.dat --soloCBposition 0_0_2_-1 3_1_3_8 --soloUMIposition 3_9_3_14 --soloAdapterSequence 'GAGTGATTGCTTGTGACGCCTT' --soloAdapterMismatchesNmax 1 --clipAdapterType CellRanger4 --soloUMIfiltering - --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_All --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --soloCellFilter CellRanger2.2 3000 0.99 10.0 --soloOutFormatFeaturesGeneField3 'Gene Expression' && mv Solo.out/Gene Solo.out/soloFeatures && cat <(echo \"Barcodes:\") Solo.out/Barcodes.stats <(echo \"Genes:\") Solo.out/soloFeatures/Features.stats > '/galaxy/server/database/objects/7/7/d/dataset_77d0dcc3-2430-44fa-83a4-cbc1e94dabd6.dat' && addthreads=${GALAXY_SLOTS:-2} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/8/b/d/dataset_8bde00a6-1ec4-4c4c-abfe-40ec9ba4b7b7.dat' Aligned.out.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "solo": "{\"filter\": {\"__current_case__\": 0, \"filter_type\": \"cellranger2\", \"max_min_ratio\": \"10.0\", \"max_perc\": \"0.99\", \"n_expected\": \"3000\"}, \"soloFeatures\": \"Gene\", \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"soloStrand\": \"Forward\", \"soloUMIfiltering\": \"-\"}", "sc": "{\"__current_case__\": 1, \"cb_whitelists\": [{\"__index__\": 0, \"cb_end_anchor\": \"2\", \"cb_end_anchor_pos\": \"-1\", \"cb_start_anchor\": \"0\", \"cb_start_anchor_pos\": \"0\", \"whitelist_file\": {\"values\": [{\"id\": 368, \"src\": \"hda\"}]}}, {\"__index__\": 1, \"cb_end_anchor\": \"3\", \"cb_end_anchor_pos\": \"8\", \"cb_start_anchor\": \"3\", \"cb_start_anchor_pos\": \"1\", \"whitelist_file\": {\"values\": [{\"id\": 369, \"src\": \"hda\"}]}}], \"clipAdapterType\": \"CellRanger4\", \"input_types\": {\"__current_case__\": 0, \"input1\": {\"values\": [{\"id\": 366, \"src\": \"hda\"}]}, \"input2\": {\"values\": [{\"id\": 367, \"src\": \"hda\"}]}, \"use\": \"repeat\"}, \"soloAdapterMismatchesNmax\": \"1\", \"soloAdapterSequence\": \"GAGTGATTGCTTGTGACGCCTT\", \"soloCBmatchWLtype\": \"1MM\", \"soloUMIdedup\": \"1MM_All\", \"solo_type\": \"CB_UMI_Complex\", \"umi_end_anchor\": \"3\", \"umi_end_anchor_pos\": \"14\", \"umi_start_anchor\": \"3\", \"umi_start_anchor_pos\": \"9\"}", "refGenomeSource": "{\"__current_case__\": 1, \"geneSource\": \"history\", \"genomeFastaFiles\": {\"values\": [{\"id\": 370, \"src\": \"hda\"}]}, \"genomeSAindexNbases\": \"4\", \"sjdbGTFfile\": {\"values\": [{\"id\": 365, \"src\": \"hda\"}]}, \"sjdbOverhang\": \"100\"}"}, "inputs": {"refGenomeSource|genomeFastaFiles": {"id": "a600e72a1eaed9d5", "src": "hda", "uuid": "4d2a3aba-6a44-4169-8525-772a46846cee"}, "refGenomeSource|sjdbGTFfile": {"id": "846ffe24b03641b2", "src": "hda", "uuid": "f38d8870-e0b7-476b-bf54-c8abfe3b2125"}, "sc|input_types|input1": {"id": "9ff6042cd60b7057", "src": "hda", "uuid": "9fda1f18-2f67-4046-bf7d-e1afc5f02467"}, "sc|input_types|input11": {"id": "9ff6042cd60b7057", "src": "hda", "uuid": "9fda1f18-2f67-4046-bf7d-e1afc5f02467"}, "sc|input_types|input2": {"id": "50ab40971672b37c", "src": "hda", "uuid": "f4cfd952-e970-4021-8a20-33ae6eafa10c"}, "sc|input_types|input21": {"id": "50ab40971672b37c", "src": "hda", "uuid": "f4cfd952-e970-4021-8a20-33ae6eafa10c"}, "sc|cb_whitelists_0|whitelist_file": {"id": "b6b30d78304c60e5", "src": "hda", "uuid": "906ecbf4-fa5e-4c09-9410-bad4028dfe67"}, "sc|cb_whitelists_1|whitelist_file": {"id": "bf62718d3a20ff23", "src": "hda", "uuid": "8327c0f3-f5b8-459e-a030-eaef47d4e306"}}, "outputs": {"output_log": {"id": "979348a5a0d3c9f2", "src": "hda", "uuid": "82398f0b-5d95-4458-b46b-b366f23671bc"}, "output_genes_filtered": {"id": "f148dc0513eb1566", "src": "hda", "uuid": "ae5dd978-08cb-446b-8c89-d791efd2688a"}, "output_barcodes_filtered": {"id": "a5d9e0c33d85ffcb", "src": "hda", "uuid": "4f831748-6efb-412e-9d93-f283cd5b3339"}, "output_matrix_filtered": {"id": "dbe0b157c77c0a7f", "src": "hda", "uuid": "90b0d454-d83e-477e-a97a-95373c88cab0"}, "output_BAM": {"id": "c1cc429ba871f337", "src": "hda", "uuid": "8bde00a6-1ec4-4c4c-abfe-40ec9ba4b7b7"}, "output_stats": {"id": "99f8cf4b9e420d72", "src": "hda", "uuid": "77d0dcc3-2430-44fa-83a4-cbc1e94dabd6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Sep 23 07:35:48 ..... started STAR run\nSep 23 07:35:48 ... starting to generate Genome files\nSep 23 07:35:48 ..... processing annotations GTF\nSep 23 07:35:48 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:35:48 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:35:48 ... loading chunks from disk, packing SA...\nSep 23 07:35:48 ... finished generating suffix array\nSep 23 07:35:48 ... generating Suffix Array index\nSep 23 07:35:48 ... completed Suffix Array index\nSep 23 07:35:48 ..... inserting junctions into the genome indices\nSep 23 07:35:48 ... writing Genome to disk ...\nSep 23 07:35:48 ... writing Suffix Array to disk ...\nSep 23 07:35:48 ... writing SAindex to disk\nSep 23 07:35:48 ..... finished successfully\nSep 23 07:35:48 ..... started STAR run\nSep 23 07:35:48 ..... loading genome\nSep 23 07:35:48 ..... started mapping\nSep 23 07:35:49 ..... finished mapping\nSep 23 07:35:49 ..... started Solo counting\nSep 23 07:35:49 ..... finished Solo counting\nSep 23 07:35:49 ..... finished successfully\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Sep 23 07:35:48 ..... started STAR run\nSep 23 07:35:48 ... starting to generate Genome files\nSep 23 07:35:48 ..... processing annotations GTF\nSep 23 07:35:48 ... starting to sort Suffix Array. This may take a long time...\nSep 23 07:35:48 ... sorting Suffix Array chunks and saving them to disk...\nSep 23 07:35:48 ... loading chunks from disk, packing SA...\nSep 23 07:35:48 ... finished generating suffix array\nSep 23 07:35:48 ... generating Suffix Array index\nSep 23 07:35:48 ... completed Suffix Array index\nSep 23 07:35:48 ..... inserting junctions into the genome indices\nSep 23 07:35:48 ... writing Genome to disk ...\nSep 23 07:35:48 ... writing Suffix Array to disk ...\nSep 23 07:35:48 ... writing SAindex to disk\nSep 23 07:35:48 ..... finished successfully\nSep 23 07:35:48 ..... started STAR run\nSep 23 07:35:48 ..... loading genome\nSep 23 07:35:48 ..... started mapping\nSep 23 07:35:49 ..... finished mapping\nSep 23 07:35:49 ..... started Solo counting\nSep 23 07:35:49 ..... finished Solo counting\nSep 23 07:35:49 ..... finished successfully\n", "stderr": "[bam_sort_core] merging from 0 files and 3 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-23 07:35:49", "plugin": "core", "name": "end_epoch", "raw_value": "1727076949.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:35:47", "plugin": "core", "name": "start_epoch", "raw_value": "1727076947.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "rna_starsolo/2.7.8a-6", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 6, "time_seconds": 33.490562200546265, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "rna_starsolo/2.7.8a-7", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 7, "time_seconds": 86.47165703773499, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "rna_starsolo/2.7.8a-7", "has_data": true, "data": {"tool_id": "rna_starsolo", "tool_version": "2.7.8a", "test_index": 7, "time_seconds": 87.56474018096924, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "samtools_split/1.9-0", "has_data": true, "data": {"tool_id": "samtools_split", "tool_version": "1.9", "test_index": 0, "time_seconds": 38.06095051765442, "inputs": {"input_bam": {"src": "hda", "id": "2b34c5dbcb9801a8"}}, "job": {"model_class": "Job", "id": "0adc3bd0aef531f6", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:03:20.895016", "update_time": "2024-09-23T08:03:37.205812", "galaxy_version": "24.1", "external_id": "gxy-c8krp", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools split -f 'Read_Group_%!.bam' -u '/galaxy/server/database/objects/1/3/2/dataset_132ed31e-3bb5-42bd-8844-c30d52c3417a.dat' -@ $addthreads '/galaxy/server/database/objects/5/d/c/dataset_5dc5f1b0-d2b1-4512-aa2e-ecf11030e156.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "header": null}, "inputs": {"input_bam": {"id": "2b34c5dbcb9801a8", "src": "hda", "uuid": "5dc5f1b0-d2b1-4512-aa2e-ecf11030e156"}}, "outputs": {"__new_primary_file_output|Mouse__": {"id": "9b76c81c3df16c98", "src": "hda", "uuid": "88a8c1e2-95e5-451b-936f-230724eb5023"}, "__new_primary_file_output|Human__": {"id": "4b42c16053007162", "src": "hda", "uuid": "3a52a07e-ce49-4141-954f-a26a5040d798"}, "__new_primary_file_output|Elephant__": {"id": "ad373da658fe2f69", "src": "hda", "uuid": "6ecff2a4-1d29-4265-b3f9-161ce524428b"}, "output": {"id": "8e613da00bf08a3d", "src": "hda", "uuid": "132ed31e-3bb5-42bd-8844-c30d52c3417a"}}, "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": "2024-09-23 08:03:25", "plugin": "core", "name": "end_epoch", "raw_value": "1727078605.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:03:25", "plugin": "core", "name": "start_epoch", "raw_value": "1727078605.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Primary output output: different than expected, difference (using diff):\n( /tmp/local_bam_converted_to_sam_szmn9tua.sam v. /tmp/history_bam_converted_to_sam_0ie75t64.sam )\n--- local_file\n+++ history_data\n@@ -6,11 +6,11 @@\n @PG\tID:bowtie2-D76CD0\tPN:bowtie2\tVN:2.1.0\n @PG\tID:bowtie2-58C6F748\tPN:bowtie2\tVN:2.1.0\n @PG\tID:bowtie2-D76CD0-8B37AF2\tPN:bowtie2\tVN:2.1.0\n-@PG\tID:samtools\tPN:samtools\tPP:bowtie2\tVN:1.9\tCL:samtools split -f Read_Group_%!.bam -u /tmp/tmpZSM0ep/files/000/dataset_2.dat /tmp/tmpZSM0ep/files/000/dataset_1.dat\n-@PG\tID:samtools.1\tPN:samtools\tPP:bowtie2-31DAC016\tVN:1.9\tCL:samtools split -f Read_Group_%!.bam -u /tmp/tmpZSM0ep/files/000/dataset_2.dat 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/galaxy/server/database/objects/1/3/2/dataset_132ed31e-3bb5-42bd-8844-c30d52c3417a.dat -@ 0 /galaxy/server/database/objects/5/d/c/dataset_5dc5f1b0-d2b1-4512-aa2e-ecf11030e156.dat\n+@PG\tID:samtools.2\tPN:samtools\tPP:bowtie2-D76CD0\tVN:1.9\tCL:samtools split -f Read_Group_%!.bam -u /galaxy/server/database/objects/1/3/2/dataset_132ed31e-3bb5-42bd-8844-c30d52c3417a.dat -@ 0 /galaxy/server/database/objects/5/d/c/dataset_5dc5f1b0-d2b1-4512-aa2e-ecf11030e156.dat\n+@PG\tID:samtools.3\tPN:samtools\tPP:bowtie2-58C6F748\tVN:1.9\tCL:samtools split -f Read_Group_%!.bam -u /galaxy/server/database/objects/1/3/2/dataset_132ed31e-3bb5-42bd-8844-c30d52c3417a.dat -@ 0 /galaxy/server/database/objects/5/d/c/dataset_5dc5f1b0-d2b1-4512-aa2e-ecf11030e156.dat\n+@PG\tID:samtools.4\tPN:samtools\tPP:bowtie2-D76CD0-8B37AF2\tVN:1.9\tCL:samtools split -f Read_Group_%!.bam -u /galaxy/server/database/objects/1/3/2/dataset_132ed31e-3bb5-42bd-8844-c30d52c3417a.dat -@ 0 /galaxy/server/database/objects/5/d/c/dataset_5dc5f1b0-d2b1-4512-aa2e-ecf11030e156.dat\n phiX174_9_527_1:0:0_0:0:0_54/1\t0\tphiX174\t9\t42\t70M\t*\t0\t0\tTCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATCAAGC\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:65A4\tYT:Z:UU\tRG:Z:Mouse\n phiX174_71_657_0:0:0_1:0:0_72/1\t0\tphiX174\t71\t42\t70M\t*\t0\t0\tGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYT:Z:UU\tRG:Z:Mouse\n phiX174_99_617_1:0:0_2:1:0_a2/1\t0\tphiX174\t99\t42\t70M\t*\t0\t0\tTACGAATTAAATCGAAGTGGACTGCTTGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:26G43\tYT:Z:UU\tRG:Z:Mouse\n"], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-0", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 0, "time_seconds": 37.316665172576904, "inputs": {"input": {"src": "hda", "id": "abab960c26557c9c"}}, "job": {"model_class": "Job", "id": "a2c05ef4a0017263", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:48:17.828608", "update_time": "2024-09-23T07:48:34.842455", "galaxy_version": "24.1", "external_id": "gxy-m47jv", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/1/3/c/dataset_13c3181d-cff9-4a99-8915-1656a0fd61c1.dat' infile && samtools view -@ $addthreads -b -o outfile infile && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "abab960c26557c9c", "src": "hda", "uuid": "13c3181d-cff9-4a99-8915-1656a0fd61c1"}}, "outputs": {"outputsam": {"id": "0896e48c590f9eb5", "src": "hda", "uuid": "12b24556-71b0-4f11-82c4-db7025e22db7"}}, "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": "2024-09-23 07:48:22", "plugin": "core", "name": "end_epoch", "raw_value": "1727077702.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:48:22", "plugin": "core", "name": "start_epoch", "raw_value": "1727077702.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (sam_to_bam_out1.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-1", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 1, "status": "skip"}}, {"id": "samtools_view/1.9+galaxy3-10", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 10, "time_seconds": 33.428306579589844, "inputs": {"input": {"src": "hda", "id": "c8cf88458eeb2a17"}, "mode|output_options|output_format|with_header": true, "mode|output_options|output_format|oformat": "sam"}, "job": {"model_class": "Job", "id": "327c66d5ff3a6469", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:53:28.775691", "update_time": "2024-09-23T07:53:41.540369", "galaxy_version": "24.1", "external_id": "gxy-8h6v9", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/6/9/4/dataset_694652d3-9b94-41f0-9793-0dce265b966d.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/e/5/5/metadata_e55b6d77-5e9a-44d9-b355-b25cb3faa13c.dat' infile.bai && samtools view -@ $addthreads -h -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 1, \"oformat\": \"sam\", \"with_header\": true}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "c8cf88458eeb2a17", "src": "hda", "uuid": "694652d3-9b94-41f0-9793-0dce265b966d"}}, "outputs": {"outputsam": {"id": "6430b1768246f8b1", "src": "hda", "uuid": "f98fbeca-86c5-4b52-9377-ab3c74e0b51c"}}, "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": "2024-09-23 07:53:30", "plugin": "core", "name": "end_epoch", "raw_value": "1727078010.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:53:30", "plugin": "core", "name": "start_epoch", "raw_value": "1727078010.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (bam_to_sam_out1.sam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-11", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 11, "time_seconds": 33.50927400588989, "inputs": {"input": {"src": "hda", "id": "8ed35ebd53f60245"}, "mode|output_options|output_format|oformat": "sam", "mode|outtype": "header"}, "job": {"model_class": "Job", "id": "47fa0a5876f8dd81", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:54:01.974838", "update_time": "2024-09-23T07:54:15.150666", "galaxy_version": "24.1", "external_id": "gxy-4d5gv", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/a/3/3/dataset_a33c10fb-05a5-45c0-9208-dc71b5607e5f.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/b/2/e/metadata_b2e32467-e664-4691-a57b-df8706213728.dat' infile.bai && samtools view -H -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 2, \"output_options\": {\"__current_case__\": 0, \"output_format\": {\"__current_case__\": 1, \"oformat\": \"sam\"}, \"reads_report_type\": \"\"}, \"outtype\": \"header\"}"}, "inputs": {"input": {"id": "8ed35ebd53f60245", "src": "hda", "uuid": "a33c10fb-05a5-45c0-9208-dc71b5607e5f"}}, "outputs": {"outputsam": {"id": "bea335e7f5201bd4", "src": "hda", "uuid": "3c042740-1cbc-4c26-81d2-bd640719be9e"}}, "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": "2024-09-23 07:54:03", "plugin": "core", "name": "end_epoch", "raw_value": "1727078043.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:54:03", "plugin": "core", "name": "start_epoch", "raw_value": "1727078043.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (bam_to_sam_out2.sam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-12", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 12, "time_seconds": 34.72643303871155, "inputs": {"input": {"src": "hda", "id": "b5a57aa17b776e1c"}, "mode|output_options|output_format|with_header": false, "mode|output_options|output_format|oformat": "sam"}, "job": {"model_class": "Job", "id": "116983429b28d5c4", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:54:36.259425", "update_time": "2024-09-23T07:54:50.110537", "galaxy_version": "24.1", "external_id": "gxy-wlc86", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/1/9/b/dataset_19b5d865-5255-4136-9f1f-ad68bae9ac49.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/1/8/6/metadata_186d6f1b-6f72-4fd5-9e88-df61cc11d988.dat' infile.bai && samtools view -@ $addthreads -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 1, \"oformat\": \"sam\", \"with_header\": false}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "b5a57aa17b776e1c", "src": "hda", "uuid": "19b5d865-5255-4136-9f1f-ad68bae9ac49"}}, "outputs": {"outputsam": {"id": "8728a18b1c104dc7", "src": "hda", "uuid": "71e01b4f-a042-4776-b86d-194011481082"}}, "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": "2024-09-23 07:54:38", "plugin": "core", "name": "end_epoch", "raw_value": "1727078078.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:54:38", "plugin": "core", "name": "start_epoch", "raw_value": "1727078078.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (bam_to_sam_out3.sam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-13", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 13, "time_seconds": 33.32422351837158, "inputs": {"input": {"src": "hda", "id": "8590b6d4b722c2c8"}, "mode|output_options|reads_report_type": "count", "mode|outtype": "all_reads"}, "job": {"model_class": "Job", "id": "d0e1e7055efd58d5", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:55:10.696718", "update_time": "2024-09-23T07:55:23.413951", "galaxy_version": "24.1", "external_id": "gxy-lqhdn", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/0/3/f/dataset_03f9dd99-46a0-443b-8ee2-b4c0547c853b.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/d/8/9/metadata_d891378e-ed6b-45e9-8a10-281db68e4b2d.dat' infile.bai && samtools view -@ $addthreads -c -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 1, \"reads_report_type\": \"count\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "8590b6d4b722c2c8", "src": "hda", "uuid": "03f9dd99-46a0-443b-8ee2-b4c0547c853b"}}, "outputs": {"outputcnt": {"id": "f314f9ad1becdda9", "src": "hda", "uuid": "232aa63d-91f4-404d-a10c-9de77b5792b9"}}, "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": "2024-09-23 07:55:12", "plugin": "core", "name": "end_epoch", "raw_value": "1727078112.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:55:11", "plugin": "core", "name": "start_epoch", "raw_value": "1727078111.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputcnt: Test output file (test_counts.tab) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-14", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 14, "time_seconds": 34.49068641662598, "inputs": {"input": {"src": "hda", "id": "6a40f3901df340d8"}, "mode|filter_config|cond_region|select_region": "no", "mode|output_options|output_format|oformat": "cram", "mode|outtype": "selected_reads", "addref_cond|ref": {"src": "hda", "id": "fbe5ce25cbc21202"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "8878c7f506391789", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:55:44.880379", "update_time": "2024-09-23T07:55:58.009467", "galaxy_version": "24.1", "external_id": "gxy-t5qvx", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/d/2/7/dataset_d278d050-daff-46f5-8a45-e22314f6837c.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/d/e/1/dataset_de1d1355-a03b-4f34-a9a3-c61e54d8689e.dat' infile && samtools view -@ $addthreads -C -o outfile --output-fmt-option no_ref -T 'reference.fa' -t 'reference.fa.fai' infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 518, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 3, \"oformat\": \"cram\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": \"\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"input": {"id": "6a40f3901df340d8", "src": "hda", "uuid": "de1d1355-a03b-4f34-a9a3-c61e54d8689e"}, "addref_cond|ref": {"id": "fbe5ce25cbc21202", "src": "hda", "uuid": "d278d050-daff-46f5-8a45-e22314f6837c"}}, "outputs": {"outputsam": {"id": "52b51851885b8cae", "src": "hda", "uuid": "b20e7a6a-e923-4200-a67a-a7b6ae974920"}}, "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": "2024-09-23 07:55:46", "plugin": "core", "name": "end_epoch", "raw_value": "1727078146.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:55:46", "plugin": "core", "name": "start_epoch", "raw_value": "1727078146.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.cram) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-15", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 15, "time_seconds": 35.79322099685669, "inputs": {"input": {"src": "hda", "id": "75a2c65b953d66fd"}, "mode|filter_config|cond_region|select_region": "no", "mode|output_options|output_format|oformat": "cram", "mode|outtype": "selected_reads", "addref_cond|ref": {"src": "hda", "id": "df8353edcf87cb89"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "c70c9892e34a53e5", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:56:19.771990", "update_time": "2024-09-23T07:56:33.899829", "galaxy_version": "24.1", "external_id": "gxy-6cwcr", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/c/b/9/dataset_cb9b92b2-0f4e-4222-bb98-32e3740f7621.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/1/d/a/dataset_1da5d665-8c2b-43b8-b756-611aaa7d6b14.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/e/5/0/metadata_e502d2bc-28f6-41a5-8c0f-f5333d6b46d9.dat' infile.bai && samtools view -@ $addthreads -C -o outfile --output-fmt-option no_ref -T 'reference.fa' -t 'reference.fa.fai' infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 521, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 3, \"oformat\": \"cram\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": \"\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"addref_cond|ref": {"id": "df8353edcf87cb89", "src": "hda", "uuid": "cb9b92b2-0f4e-4222-bb98-32e3740f7621"}, "input": {"id": "75a2c65b953d66fd", "src": "hda", "uuid": "1da5d665-8c2b-43b8-b756-611aaa7d6b14"}}, "outputs": {"outputsam": {"id": "76fe332a115b147e", "src": "hda", "uuid": "63142120-9131-4ff6-a3c4-2b67ec869b12"}}, "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": "2024-09-23 07:56:22", "plugin": "core", "name": "end_epoch", "raw_value": "1727078182.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:56:22", "plugin": "core", "name": "start_epoch", "raw_value": "1727078182.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.cram) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-16", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 16, "status": "skip"}}, {"id": "samtools_view/1.9+galaxy3-17", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 17, "time_seconds": 34.191972732543945, "inputs": {"input": {"src": "hda", "id": "7709ce5f8c2e8869"}, "mode|filter_config|cond_region|regions": "CHROMOSOME_I", "mode|filter_config|cond_region|select_region": "text", "mode|output_options|output_format|oformat": "cram", "mode|outtype": "selected_reads", "addref_cond|ref": {"src": "hda", "id": "82e36a11925fd97a"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "554b4bbc54bfaf13", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:56:54.863667", "update_time": "2024-09-23T07:57:08.363061", "galaxy_version": "24.1", "external_id": "gxy-rg7x8", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/f/d/2/dataset_fd2b8e5b-8621-4b71-b6ff-8cf76d54ef2a.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/1/3/c/dataset_13cd95f7-2a99-47ab-bf43-80c688bf8cd6.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/9/e/5/metadata_9e5d28fd-5982-4cf5-a772-d1a9c27e04bb.dat' infile.bai && samtools view -@ $addthreads -C -o outfile --output-fmt-option no_ref -T 'reference.fa' -t 'reference.fa.fai' infile 'CHROMOSOME_I'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 524, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 1, \"regions\": \"CHROMOSOME_I\", \"select_region\": \"text\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 3, \"oformat\": \"cram\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": \"\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"addref_cond|ref": {"id": "82e36a11925fd97a", "src": "hda", "uuid": "fd2b8e5b-8621-4b71-b6ff-8cf76d54ef2a"}, "input": {"id": "7709ce5f8c2e8869", "src": "hda", "uuid": "13cd95f7-2a99-47ab-bf43-80c688bf8cd6"}}, "outputs": {"outputsam": {"id": "5892518571322e62", "src": "hda", "uuid": "7c1febb6-7e0c-4b3d-9944-8b89a27bb416"}}, "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": "2024-09-23 07:56:57", "plugin": "core", "name": "end_epoch", "raw_value": "1727078217.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:56:56", "plugin": "core", "name": "start_epoch", "raw_value": "1727078216.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.cram) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-18", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 18, "time_seconds": 36.89895987510681, "inputs": {"input": {"src": "hda", "id": "12e578cd7a8a86ff"}, "mode|filter_config|cond_region|regions": "CHROMOSOME_I", "mode|filter_config|cond_region|select_region": "text", "mode|output_options|output_format|oformat": "bam", "mode|outtype": "selected_reads", "addref_cond|ref": {"src": "hda", "id": "90948cb305f2303e"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "b3a11f08b11e805f", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:57:30.736009", "update_time": "2024-09-23T07:57:45.139878", "galaxy_version": "24.1", "external_id": "gxy-w752p", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/8/a/a/dataset_8aa63d94-a5cd-4445-a9a6-6668b439ecf6.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/c/c/1/dataset_cc130036-5dfc-46d1-af66-2ad745f4e26a.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/f/1/f/metadata_f1f2b00c-7ec9-47a1-9f09-d15948fe0a53.dat' infile.crai && samtools view -@ $addthreads -b -o outfile -T 'reference.fa' -t 'reference.fa.fai' infile 'CHROMOSOME_I' && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"cram\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 527, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 1, \"regions\": \"CHROMOSOME_I\", \"select_region\": \"text\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": \"\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"addref_cond|ref": {"id": "90948cb305f2303e", "src": "hda", "uuid": "8aa63d94-a5cd-4445-a9a6-6668b439ecf6"}, "input": {"id": "12e578cd7a8a86ff", "src": "hda", "uuid": "cc130036-5dfc-46d1-af66-2ad745f4e26a"}}, "outputs": {"outputsam": {"id": "53101be3f95efd2a", "src": "hda", "uuid": "df3c9ba8-ae83-458e-8972-233038b29a00"}}, "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": "2024-09-23 07:57:33", "plugin": "core", "name": "end_epoch", "raw_value": "1727078253.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:57:32", "plugin": "core", "name": "start_epoch", "raw_value": "1727078252.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-19", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 19, "time_seconds": 38.207602739334106, "inputs": {"input": {"src": "hda", "id": "a37dd77c8bbdb148"}, "mode|filter_config|cond_region|bedfile": {"src": "hda", "id": "09f30b0bfb5a805c"}, "mode|filter_config|cond_region|select_region": "bed", "mode|output_options|output_format|oformat": "bam", "mode|outtype": "selected_reads", "addref_cond|ref": {"src": "hda", "id": "26ab1501f4d571f6"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "40f9c51263393d0f", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:58:10.330386", "update_time": "2024-09-23T07:58:23.626299", "galaxy_version": "24.1", "external_id": "gxy-h5rjm", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/d/5/f/dataset_d5fa2b70-dacf-4870-aa12-9f5adac13b02.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/7/f/f/dataset_7ff13f58-9df7-4543-958a-37294548f513.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/2/d/b/metadata_2dbf10f1-456d-4439-98b2-a533875ffdc3.dat' infile.crai && samtools view -@ $addthreads -b -L '/galaxy/server/database/objects/2/5/d/dataset_25de10c4-df8b-4d38-872b-b71dc92ef9dd.dat' -o outfile -T 'reference.fa' -t 'reference.fa.fai' infile && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"cram\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 531, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 2, \"bedfile\": {\"values\": [{\"id\": 530, \"src\": \"hda\"}]}, \"select_region\": \"bed\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": \"\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"addref_cond|ref": {"id": "26ab1501f4d571f6", "src": "hda", "uuid": "d5fa2b70-dacf-4870-aa12-9f5adac13b02"}, "mode|filter_config|cond_region|bedfile": {"id": "09f30b0bfb5a805c", "src": "hda", "uuid": "25de10c4-df8b-4d38-872b-b71dc92ef9dd"}, "input": {"id": "a37dd77c8bbdb148", "src": "hda", "uuid": "7ff13f58-9df7-4543-958a-37294548f513"}}, "outputs": {"outputsam": {"id": "a9c4cc18b0e255a3", "src": "hda", "uuid": "efbf85d8-e4f5-4e85-8abc-8c35d4854b9a"}}, "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": "2024-09-23 07:58:12", "plugin": "core", "name": "end_epoch", "raw_value": "1727078292.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:58:12", "plugin": "core", "name": "start_epoch", "raw_value": "1727078292.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-2", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 2, "time_seconds": 34.52001905441284, "inputs": {"input": {"src": "hda", "id": "2960dbfd59324cd4"}, "addref_cond|ref": {"src": "hda", "id": "76ee67b30718331a"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "c0234df653c5db45", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:48:55.902110", "update_time": "2024-09-23T07:49:09.389120", "galaxy_version": "24.1", "external_id": "gxy-fxjmn", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/5/f/6/dataset_5f601e29-36b6-44b1-93e1-0e459de07813.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/b/0/a/dataset_b0a593b0-1972-4900-b1aa-0298f2d7a111.dat' infile && samtools view -@ $addthreads -b -o outfile -T 'reference.fa' -t 'reference.fa.fai' infile && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"equCab2\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/equCab2.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 492, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "2960dbfd59324cd4", "src": "hda", "uuid": "b0a593b0-1972-4900-b1aa-0298f2d7a111"}, "addref_cond|ref": {"id": "76ee67b30718331a", "src": "hda", "uuid": "5f601e29-36b6-44b1-93e1-0e459de07813"}}, "outputs": {"outputsam": {"id": "467a7955944ca38c", "src": "hda", "uuid": "1c12e418-4f40-466a-b686-00abe1780133"}}, "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": "2024-09-23 07:48:58", "plugin": "core", "name": "end_epoch", "raw_value": "1727077738.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:48:58", "plugin": "core", "name": "start_epoch", "raw_value": "1727077738.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (sam_to_bam_out3.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-20", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 20, "time_seconds": 33.957026958465576, "inputs": {"input": {"src": "hda", "id": "c33decec615711d9"}, "mode|subsample_config|subsampling_mode|target": "2", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "3794a20af6d34e2d", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:58:44.400151", "update_time": "2024-09-23T07:58:57.748589", "galaxy_version": "24.1", "external_id": "gxy-h8gnn", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/6/a/2/dataset_6a299996-4119-43b9-b5e7-9814fe255ec8.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/2; print(frac > 1 ? 28010+1/frac : \".0\")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"\", \"select_subsample\": \"target\", \"target\": \"2\"}}}"}, "inputs": {"input": {"id": "c33decec615711d9", "src": "hda", "uuid": "6a299996-4119-43b9-b5e7-9814fe255ec8"}}, "outputs": {"outputsam": {"id": "ece0a938c41ee079", "src": "hda", "uuid": "0e7f26b7-fd67-4a5c-9e48-53d3a6823135"}}, "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": "2024-09-23 07:58:46", "plugin": "core", "name": "end_epoch", "raw_value": "1727078326.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:58:46", "plugin": "core", "name": "start_epoch", "raw_value": "1727078326.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test_ds.sam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-21", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 21, "time_seconds": 33.17033624649048, "inputs": {"input": {"src": "hda", "id": "fa940a34a405fafa"}, "mode|subsample_config|subsampling_mode|target": "20", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "0308a5f7176b3907", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:59:18.358454", "update_time": "2024-09-23T07:59:30.977166", "galaxy_version": "24.1", "external_id": "gxy-l9hf8", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/9/5/4/dataset_954be9a5-1516-4b2b-97e2-477881a9cdba.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/20; print(frac > 1 ? 12740+1/frac : \".0\")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"\", \"select_subsample\": \"target\", \"target\": \"20\"}}}"}, "inputs": {"input": {"id": "fa940a34a405fafa", "src": "hda", "uuid": "954be9a5-1516-4b2b-97e2-477881a9cdba"}}, "outputs": {"outputsam": {"id": "a1ada1392571a2d5", "src": "hda", "uuid": "63dfe45c-a327-4840-b2a7-e5b2aadaf019"}}, "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": "2024-09-23 07:59:19", "plugin": "core", "name": "end_epoch", "raw_value": "1727078359.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:59:19", "plugin": "core", "name": "start_epoch", "raw_value": "1727078359.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.sam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-22", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 22, "time_seconds": 24.766925573349, "inputs": {"input": {"src": "hda", "id": "9ba29b32212e9193"}, "mode|subsample_config|subsampling_mode|target": "20", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "363809241d2e2d64", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "error", "exit_code": null, "create_time": "2024-09-23T07:59:50.616480", "update_time": "2024-09-23T07:59:55.788130", "galaxy_version": "24.1", "external_id": "gxy-bvgp9", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/4/d/2/dataset_4d2d6f9a-a69a-442d-922d-4a8a589f2557.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/20; print(frac > 1 ? 6776+1/frac : \".0\")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"\", \"select_subsample\": \"target\", \"target\": \"20\"}}}"}, "inputs": {"input": {"id": "9ba29b32212e9193", "src": "hda", "uuid": "4d2d6f9a-a69a-442d-922d-4a8a589f2557"}}, "outputs": {"outputsam": {"id": "8e06e5b36898b515", "src": "hda", "uuid": "64ee866e-0707-46e5-bd5b-73a833baf83c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-23", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 23, "time_seconds": 13.64070200920105, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "samtools_view/1.9+galaxy3-24", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 24, "time_seconds": 34.20408511161804, "inputs": {"input": {"src": "hda", "id": "13c09af532959d32"}, "mode|subsample_config|subsampling_mode|target": "2", "mode|subsample_config|subsampling_mode|seed": "7", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "1a49bfec6f972a4d", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:00:30.087922", "update_time": "2024-09-23T08:00:43.613942", "galaxy_version": "24.1", "external_id": "gxy-224h2", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/1/3/a/dataset_13a30497-0fe6-4aa0-884a-27c945b2574b.dat' infile && sample_fragment=`samtools view -c infile | awk '{s=$1} END {frac=s/2; print(frac > 1 ? 7+1/frac : \".0\")}'` && samtools view -@ $addthreads -h -s ${sample_fragment} -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"7\", \"select_subsample\": \"target\", \"target\": \"2\"}}}"}, "inputs": {"input": {"id": "13c09af532959d32", "src": "hda", "uuid": "13a30497-0fe6-4aa0-884a-27c945b2574b"}}, "outputs": {"outputsam": {"id": "d325fcc4b96d7f00", "src": "hda", "uuid": "3e6bd64c-a941-46ea-ad8a-5e25c8b9b4e1"}}, "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": "2024-09-23 08:00:31", "plugin": "core", "name": "end_epoch", "raw_value": "1727078431.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:00:31", "plugin": "core", "name": "start_epoch", "raw_value": "1727078431.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test_ds.sam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-25", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 25, "time_seconds": 32.43666863441467, "inputs": {"input": {"src": "hda", "id": "4c4ce7b94f80ece9"}, "mode|subsample_config|subsampling_mode|target": "2", "mode|subsample_config|subsampling_mode|seed": "7", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "63202692711a29c2", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:01:03.221147", "update_time": "2024-09-23T08:01:16.083990", "galaxy_version": "24.1", "external_id": "gxy-r6k96", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/5/2/0/dataset_52082a4e-fed3-4c8f-8d4e-d4af8d4e1720.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/a/6/d/metadata_a6d41eca-87bc-4ec7-acba-f233f42dba1d.dat' infile.bai && sample_fragment=`samtools idxstats infile | awk '{s+=$4+$3} END {frac=s/2; print(frac > 1 ? 7+1/frac : \".0\")}'` && samtools view -@ $addthreads -b -s ${sample_fragment} -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"7\", \"select_subsample\": \"target\", \"target\": \"2\"}}}"}, "inputs": {"input": {"id": "4c4ce7b94f80ece9", "src": "hda", "uuid": "52082a4e-fed3-4c8f-8d4e-d4af8d4e1720"}}, "outputs": {"outputsam": {"id": "a191515295ca77bb", "src": "hda", "uuid": "395ffe7f-ce4d-4187-bf8e-35bacd8aeca2"}}, "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": "2024-09-23 08:01:04", "plugin": "core", "name": "end_epoch", "raw_value": "1727078464.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:01:04", "plugin": "core", "name": "start_epoch", "raw_value": "1727078464.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test_ds.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-26", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 26, "time_seconds": 34.284464597702026, "inputs": {"input": {"src": "hda", "id": "e45c5ec8b4942fff"}, "mode|subsample_config|subsampling_mode|target": "20", "mode|subsample_config|subsampling_mode|seed": "7", "mode|subsample_config|subsampling_mode|select_subsample": "target", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "f23cf37eb18611a1", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:01:36.562908", "update_time": "2024-09-23T08:01:50.450862", "galaxy_version": "24.1", "external_id": "gxy-ptlvd", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/1/0/0/dataset_10003c31-b77d-4020-abc6-18470fda4765.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/d/8/9/metadata_d89d0e15-5f30-480d-9781-5cf74252536a.dat' infile.bai && sample_fragment=`samtools idxstats infile | awk '{s+=$4+$3} END {frac=s/20; print(frac > 1 ? 7+1/frac : \".0\")}'` && samtools view -@ $addthreads -b -s ${sample_fragment} -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 1, \"seed\": \"7\", \"select_subsample\": \"target\", \"target\": \"20\"}}}"}, "inputs": {"input": {"id": "e45c5ec8b4942fff", "src": "hda", "uuid": "10003c31-b77d-4020-abc6-18470fda4765"}}, "outputs": {"outputsam": {"id": "52f07a746cfef027", "src": "hda", "uuid": "b39ba855-2531-4286-815e-d3b77b17e95b"}}, "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": "2024-09-23 08:01:38", "plugin": "core", "name": "end_epoch", "raw_value": "1727078498.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:01:38", "plugin": "core", "name": "start_epoch", "raw_value": "1727078498.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-27", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 27, "time_seconds": 33.295531034469604, "inputs": {"input": {"src": "hda", "id": "c93951553137d7c0"}, "mode|subsample_config|subsampling_mode|factor": "5", "mode|subsample_config|subsampling_mode|seed": "7", "mode|subsample_config|subsampling_mode|select_subsample": "fraction", "mode|output_options|output_format|oformat": "input", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "d8431777c8df900c", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:02:10.675650", "update_time": "2024-09-23T08:02:23.998486", "galaxy_version": "24.1", "external_id": "gxy-f46qh", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/6/a/1/dataset_6a1ebf8c-68c5-4d21-98c4-747160152b5e.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/d/b/5/metadata_db506423-4220-40d6-92b7-969bbe28f3ee.dat' infile.bai && samtools view -@ $addthreads -b -s 7.2 -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"5.0\", \"seed\": \"7\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"input": {"id": "c93951553137d7c0", "src": "hda", "uuid": "6a1ebf8c-68c5-4d21-98c4-747160152b5e"}}, "outputs": {"outputsam": {"id": "86c42712d4f0c26b", "src": "hda", "uuid": "4317b5ca-6a8c-459b-8c21-77d0622b0475"}}, "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": "2024-09-23 08:02:12", "plugin": "core", "name": "end_epoch", "raw_value": "1727078532.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:02:12", "plugin": "core", "name": "start_epoch", "raw_value": "1727078532.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test_ds.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-28", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 28, "time_seconds": 34.48501658439636, "inputs": {"input": {"src": "hda", "id": "1a4bb34ba2289b5c"}, "mode|subsample_config|subsampling_mode|factor": "1.25", "mode|subsample_config|subsampling_mode|seed": "7", "mode|subsample_config|subsampling_mode|select_subsample": "fraction", "mode|output_options|output_format|oformat": "input", "mode|output_options|reads_report_type": "dropped", "mode|outtype": "selected_reads"}, "job": {"model_class": "Job", "id": "e901b4616acbf4c6", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T08:02:44.481668", "update_time": "2024-09-23T08:02:58.420990", "galaxy_version": "24.1", "external_id": "gxy-wshrb", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/1/6/2/dataset_162da6a9-0b62-4452-9cee-bdc177243384.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/e/e/3/metadata_ee35198c-b164-4d70-910c-517737453ef1.dat' infile.bai && samtools view -@ $addthreads -b -s 7.8 -U outfile -o /dev/null infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 1, \"filter_config\": {\"cigarcons\": \"\", \"cond_region\": {\"__current_case__\": 0, \"select_region\": \"no\"}, \"cond_rg\": {\"__current_case__\": 0, \"select_rg\": \"no\"}, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"inclusive_filter\": null, \"library\": null, \"quality\": \"\"}, \"output_options\": {\"__current_case__\": 1, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"complementary_output\": false, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"dropped\"}, \"outtype\": \"selected_reads\", \"subsample_config\": {\"subsampling_mode\": {\"__current_case__\": 0, \"factor\": \"1.25\", \"seed\": \"7\", \"select_subsample\": \"fraction\"}}}"}, "inputs": {"input": {"id": "1a4bb34ba2289b5c", "src": "hda", "uuid": "162da6a9-0b62-4452-9cee-bdc177243384"}}, "outputs": {"outputsam": {"id": "e25232470f56c0ae", "src": "hda", "uuid": "2fc9b0ce-c2b2-48a3-a1c6-48764a504c80"}}, "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": "2024-09-23 08:02:46", "plugin": "core", "name": "end_epoch", "raw_value": "1727078566.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 08:02:46", "plugin": "core", "name": "start_epoch", "raw_value": "1727078566.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test_ds.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-3", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 3, "time_seconds": 34.408647537231445, "inputs": {"input": {"src": "hda", "id": "fa5082c6bb884e42"}, "addref_cond|ref": {"src": "hda", "id": "55f02ac416ddf283"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "afb771a7bb55e662", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:49:30.743436", "update_time": "2024-09-23T07:49:43.832112", "galaxy_version": "24.1", "external_id": "gxy-qpdlv", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/e/7/6/dataset_e76ab6f0-fad8-4269-b0b1-cd97f6340d94.dat' reference.fa && samtools faidx reference.fa && ln -s '/galaxy/server/database/objects/8/3/7/dataset_83719690-92c1-4ad0-8591-390fc0e6d3b9.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/b/7/6/metadata_b7619ed9-a1c5-48e6-acfb-4f1823e475dc.dat' infile.crai && samtools view -@ $addthreads -b -o outfile -T 'reference.fa' -t 'reference.fa.fai' infile && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"cram\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 495, \"src\": \"hda\"}]}}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "fa5082c6bb884e42", "src": "hda", "uuid": "83719690-92c1-4ad0-8591-390fc0e6d3b9"}, "addref_cond|ref": {"id": "55f02ac416ddf283", "src": "hda", "uuid": "e76ab6f0-fad8-4269-b0b1-cd97f6340d94"}}, "outputs": {"outputsam": {"id": "e526178470c5ac18", "src": "hda", "uuid": "d93b1fd9-12ea-4f54-9e74-870cd04d7640"}}, "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": "2024-09-23 07:49:32", "plugin": "core", "name": "end_epoch", "raw_value": "1727077772.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:49:32", "plugin": "core", "name": "start_epoch", "raw_value": "1727077772.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (test.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-4", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 4, "time_seconds": 34.30172896385193, "inputs": {"input": {"src": "hda", "id": "2f0fb8abea062761"}}, "job": {"model_class": "Job", "id": "97d23674f5588acb", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:50:04.300304", "update_time": "2024-09-23T07:50:18.288952", "galaxy_version": "24.1", "external_id": "gxy-ktptr", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/3/e/5/dataset_3e5ebafa-f98e-4f98-b7c1-9200bebf1f9c.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/d/a/9/metadata_da9bf3bf-8311-4763-a228-3cd06c702078.dat' infile.bai && samtools view -@ $addthreads -b -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "2f0fb8abea062761", "src": "hda", "uuid": "3e5ebafa-f98e-4f98-b7c1-9200bebf1f9c"}}, "outputs": {"outputsam": {"id": "82461786cb21b76e", "src": "hda", "uuid": "f1572bdc-ff09-4216-992f-2f44c2eff47d"}}, "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": "2024-09-23 07:50:06", "plugin": "core", "name": "end_epoch", "raw_value": "1727077806.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:50:06", "plugin": "core", "name": "start_epoch", "raw_value": "1727077806.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (1_sort.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-5", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 5, "time_seconds": 33.755908250808716, "inputs": {"input": {"src": "hda", "id": "b3da1ace1fea32ce"}, "mode|output_options|output_format|oformat": "input"}, "job": {"model_class": "Job", "id": "787e0b7b9546a7d5", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:50:38.833542", "update_time": "2024-09-23T07:50:51.939219", "galaxy_version": "24.1", "external_id": "gxy-d9nt4", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/d/5/8/dataset_d58e1324-8284-47bd-954d-d964b5ffde25.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/3/c/6/metadata_3c6b5bdc-f78d-4829-ac8b-10b2812e0bb8.dat' infile.bai && samtools view -@ $addthreads -b -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "b3da1ace1fea32ce", "src": "hda", "uuid": "d58e1324-8284-47bd-954d-d964b5ffde25"}}, "outputs": {"outputsam": {"id": "866664c30ff0ea34", "src": "hda", "uuid": "7c8946f2-986a-4970-a25f-247dd737ee5d"}}, "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": "2024-09-23 07:50:40", "plugin": "core", "name": "end_epoch", "raw_value": "1727077840.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:50:40", "plugin": "core", "name": "start_epoch", "raw_value": "1727077840.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (1_sort.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-6", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 6, "time_seconds": 34.61702537536621, "inputs": {"input": {"src": "hda", "id": "25b741412b62dab4"}}, "job": {"model_class": "Job", "id": "bc8e21ef30b30f98", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:51:13.631491", "update_time": "2024-09-23T07:51:26.729364", "galaxy_version": "24.1", "external_id": "gxy-fw7k9", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/e/d/b/dataset_edb79c32-2833-4871-b2ba-414679fb2a40.dat' infile && samtools view -@ $addthreads -b -o outfile infile && samtools sort -@ $addthreads -m $addmemory\"M\" -T \"${TMPDIR:-.}\" -O bam -o tmpsam outfile && mv tmpsam outfile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"qname_sorted.bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 2, \"oformat\": \"bam\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "25b741412b62dab4", "src": "hda", "uuid": "edb79c32-2833-4871-b2ba-414679fb2a40"}}, "outputs": {"outputsam": {"id": "404fd3831631d4fe", "src": "hda", "uuid": "3f15100c-89e8-4bc3-9767-01412f4c7adf"}}, "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": "2024-09-23 07:51:15", "plugin": "core", "name": "end_epoch", "raw_value": "1727077875.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:51:15", "plugin": "core", "name": "start_epoch", "raw_value": "1727077875.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (1_sort.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_view/1.9+galaxy3-7", "has_data": true, "data": {"tool_id": "samtools_view", "tool_version": "1.9+galaxy3", "test_index": 7, "time_seconds": 33.204936265945435, "inputs": {"input": {"src": "hda", "id": "c52da407ec69b2dc"}, "mode|output_options|output_format|oformat": "input"}, "job": {"model_class": "Job", "id": "386d0735a5dc86d3", "history_id": "abbc0a781ea0cf97", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "state": "ok", "exit_code": 0, "create_time": "2024-09-23T07:51:47.287649", "update_time": "2024-09-23T07:52:00.107648", "galaxy_version": "24.1", "external_id": "gxy-nfbp5", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/galaxy/server/database/objects/1/e/a/dataset_1eaac544-e573-4c10-9b43-c725da7bb32b.dat' infile && samtools view -@ $addthreads -h -o outfile infile", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"qname_sorted.bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "mode": "{\"__current_case__\": 0, \"output_options\": {\"__current_case__\": 0, \"adv_output\": {\"collapsecigar\": false, \"readtags\": []}, \"output_format\": {\"__current_case__\": 0, \"oformat\": \"input\"}, \"reads_report_type\": \"retained\"}, \"outtype\": \"all_reads\"}"}, "inputs": {"input": {"id": "c52da407ec69b2dc", "src": "hda", "uuid": "1eaac544-e573-4c10-9b43-c725da7bb32b"}}, "outputs": {"outputsam": {"id": "13c528b03a70a0ad", "src": "hda", "uuid": "7646663d-53be-4e2e-94b1-06273948fe6a"}}, "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": "2024-09-23 07:51:49", "plugin": "core", "name": "end_epoch", "raw_value": "1727077909.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 07:51:48", "plugin": "core", "name": "start_epoch", "raw_value": "1727077908.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output outputsam: Test output file (1_sort_read_names.bam) is missing. 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To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\nLoading required package: DelayedArray\nLoading required package: matrixStats\n\nAttaching package: 'matrixStats'\n\nThe following objects are masked from 'package:Biobase':\n\n anyMissing, rowMedians\n\nLoading required package: BiocParallel\n\nAttaching package: 'DelayedArray'\n\nThe following objects are masked from 'package:matrixStats':\n\n colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges\n\nThe following objects are masked from 'package:base':\n\n aperm, apply, rowsum\n\nLoading required package: rhdf5\nLoading required package: rtracklayer\nLoading required package: ggplot2\n\nAttaching package: 'scater'\n\nThe following object is masked from 'package:S4Vectors':\n\n rename\n\nThe following object is masked from 'package:stats':\n\n filter\n\nWarning message:\nIn .local(object, ...) : using library sizes as size factors\n", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"Normalising....\"\n[1] \"Finished normalising\"\n[1] TRUE\n", "stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\nLoading required package: parallel\n\nAttaching package: 'BiocGenerics'\n\nThe following objects are masked from 'package:parallel':\n\n clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n clusterExport, clusterMap, parApply, parCapply, parLapply,\n parLapplyLB, parRapply, parSapply, parSapplyLB\n\nThe following objects are masked from 'package:stats':\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from 'package:base':\n\n Filter, Find, Map, Position, Reduce, anyDuplicated, append,\n as.data.frame, basename, cbind, colnames, dirname, do.call,\n duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,\n lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,\n pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,\n tapply, union, unique, unsplit, which, which.max, which.min\n\n\nAttaching package: 'S4Vectors'\n\nThe following object is masked from 'package:base':\n\n expand.grid\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\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\nLoading required package: DelayedArray\nLoading required package: matrixStats\n\nAttaching package: 'matrixStats'\n\nThe following objects are masked from 'package:Biobase':\n\n anyMissing, rowMedians\n\nLoading required package: BiocParallel\n\nAttaching package: 'DelayedArray'\n\nThe following objects are masked from 'package:matrixStats':\n\n colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges\n\nThe following objects are masked from 'package:base':\n\n aperm, apply, rowsum\n\nLoading required package: rhdf5\nLoading required package: rtracklayer\nLoading required package: ggplot2\n\nAttaching package: 'scater'\n\nThe following object is masked from 'package:S4Vectors':\n\n rename\n\nThe following object is masked from 'package:stats':\n\n filter\n\nWarning message:\nIn .local(object, ...) : using library sizes as size factors\n", "job_messages": [], "dependencies": [], 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