diff --git a/reports/anvil-production/README.md b/reports/anvil-production/README.md index 56309ef85..c5bd88169 100644 --- a/reports/anvil-production/README.md +++ b/reports/anvil-production/README.md @@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the Latest tool tests for each chunk: -
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Aug 26 00:46:31 2024Mon Aug 19 00:46:07 2024
1ToolsetMon Aug 26 12:48:20 2024Mon Aug 19 12:47:26 2024
2ToolsetTue Aug 27 00:46:45 2024Tue Aug 20 00:46:51 2024
3ToolsetTue Aug 27 12:47:56 2024Tue Aug 20 12:48:20 2024
4ToolsetWed Aug 28 00:47:17 2024Wed Aug 21 00:46:14 2024
5ToolsetWed Aug 28 12:49:16 2024Wed Aug 21 12:46:44 2024
6ToolsetThu Aug 29 00:55:34 2024Thu Aug 22 00:47:23 2024
7ToolsetThu Aug 29 12:48:26 2024Thu Aug 22 12:47:28 2024
8ToolsetFri Aug 30 00:47:54 2024Fri Aug 23 00:47:58 2024
9ToolsetFri Aug 23 12:46:09 2024Fri Aug 16 12:46:51 2024
10ToolsetSat Aug 24 00:45:53 2024Sat Aug 17 00:44:44 2024
11ToolsetSat Aug 24 12:45:32 2024Sat Aug 17 12:43:09 2024
12ToolsetSun Aug 25 00:49:24 2024Sun Aug 18 00:50:18 2024
13ToolsetSun Aug 25 12:44:55 2024Sun Aug 18 12:47:05 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Aug 26 00:46:31 2024Mon Aug 19 00:46:07 2024
1ToolsetMon Aug 26 12:48:20 2024Mon Aug 19 12:47:26 2024
2ToolsetTue Aug 27 00:46:45 2024Tue Aug 20 00:46:51 2024
3ToolsetTue Aug 27 12:47:56 2024Tue Aug 20 12:48:20 2024
4ToolsetWed Aug 28 00:47:17 2024Wed Aug 21 00:46:14 2024
5ToolsetWed Aug 28 12:49:16 2024Wed Aug 21 12:46:44 2024
6ToolsetThu Aug 29 00:55:34 2024Thu Aug 22 00:47:23 2024
7ToolsetThu Aug 29 12:48:26 2024Thu Aug 22 12:47:28 2024
8ToolsetFri Aug 30 00:47:54 2024Fri Aug 23 00:47:58 2024
9ToolsetFri Aug 30 12:48:09 2024Fri Aug 23 12:46:09 2024
10ToolsetSat Aug 24 00:45:53 2024Sat Aug 17 00:44:44 2024
11ToolsetSat Aug 24 12:45:32 2024Sat Aug 17 12:43:09 2024
12ToolsetSun Aug 25 00:49:24 2024Sun Aug 18 00:50:18 2024
13ToolsetSun Aug 25 12:44:55 2024Sun Aug 18 12:47:05 2024
diff --git a/reports/anvil-production/tool-tests/chunks.json b/reports/anvil-production/tool-tests/chunks.json index 0940a76ab..4bf7b1ff1 100644 --- a/reports/anvil-production/tool-tests/chunks.json +++ b/reports/anvil-production/tool-tests/chunks.json @@ -49,11 +49,11 @@ "date2": "Tue Aug 20 00:46:51 2024" }, "9": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-23-12-31-1/results.html", - "date1": "Fri Aug 23 12:46:09 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-23-12-31-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-16-12-31-1/results.html", - "date2": "Fri Aug 16 12:46:51 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/results.html", + "date1": "Fri Aug 30 12:48:09 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-23-12-31-1/results.html", + "date2": "Fri Aug 23 12:46:09 2024" }, "13": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-25-12-29-1/results.html", diff --git a/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/chunk.json b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/chunk.json new file mode 100644 index 000000000..98163f565 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/chunk.json @@ -0,0 +1,7 @@ +{ + "9": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/results.html", + "date1": "Fri Aug 30 12:48:09 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/chunk.txt b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/chunk.txt new file mode 100644 index 000000000..4d5c5637a --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/chunk.txt @@ -0,0 +1,15 @@ +-t sqlite_to_tabular --tool-version bce29ec10b78 +-t replace_column_by_key_value_file --tool-version d533e4b75800 +-t fastqc --tool-version e7b2202befea +-t samtools_markdup --tool-version 83b8e36e9cbe +-t bamtools_filter --tool-version cb20f99fd45b +-t bcftools_cnv --tool-version 01d6b7d6365e +-t bcftools_roh --tool-version b76adb2f1c51 +-t vcfbedintersect --tool-version aea8e90ad788 +-t vcfvcfintersect --tool-version 166c4f50525f +-t poretools_hist --tool-version 5a82eb9e1b89 +-t deeptools_compute_matrix --tool-version 514fa53b5efb +-t deeptools_bam_coverage --tool-version bb1e4f63e0e6 +-t lofreq_indelqual --tool-version 426d707dfc47 +-t snpsift --tool-version 2e497a770bca +-t mummer_nucmer --tool-version 636b049e6141 diff --git a/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/6cded8ba9046fcf8.json b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/6cded8ba9046fcf8.json new file mode 100644 index 000000000..820a70f16 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/6cded8ba9046fcf8.json @@ -0,0 +1,50 @@ +{ + "model_class": "Job", + "id": "6cded8ba9046fcf8", + "state": "error", + "exit_code": null, + "update_time": "2024-08-30T12:55:13.131201", + "create_time": "2024-08-30T12:55:08.534034", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", + "history_id": "156c4392fa643bca", + "external_id": "gxy-f6mb4", + "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/9/8/8/dataset_988d51bd-daba-4ed9-a392-1ed7724aba4d.dat' && samtools markdup -@ $addthreads -r coordsort.sam '/galaxy/server/database/objects/a/6/6/dataset_a667be73-c02a-41a2-89f1-4bda7a51270c.dat'", + "traceback": null, + "params": { + "__input_ext": "\"sam\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "supp": "false", + "stats": "false", + "maxlen": "\"\"", + "remove": "true" + }, + "inputs": { + "bamfile": { + "id": "0f3b0b88fd8d3bd3", + "src": "hda", + "uuid": "988d51bd-daba-4ed9-a392-1ed7724aba4d" + } + }, + "outputs": { + "output": { + "id": "0a2d17a5e5658f2e", + "src": "hda", + "uuid": "a667be73-c02a-41a2-89f1-4bda7a51270c" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/95658726ede0b433.json b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/95658726ede0b433.json new file mode 100644 index 000000000..8c8d72dcf --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/95658726ede0b433.json @@ -0,0 +1,51 @@ +{ + "model_class": "Job", + "id": "95658726ede0b433", + "state": "error", + "exit_code": null, + "update_time": "2024-08-30T13:03:30.926638", + "create_time": "2024-08-30T13:03:24.700290", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1", + "history_id": "156c4392fa643bca", + "external_id": "gxy-qbhxr", + "command_line": "export MPLBACKEND=\"agg\" && poretools hist '/galaxy/server/database/objects/c/e/a/dataset_cea96354-2672-45e7-a710-006d866d1524.dat' --saveas histogram.svg --min-length 0 --max-length 1000000000 --num-bins 50 && mv histogram.svg '/galaxy/server/database/objects/8/3/6/dataset_836c00e8-a52e-41ff-9aed-169c2737422e.dat'", + "traceback": 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": "\"svg\"" + }, + "inputs": { + "input": { + "id": "2d284e114fa37175", + "src": "hda", + "uuid": "cea96354-2672-45e7-a710-006d866d1524" + } + }, + "outputs": { + "output": { + "id": "f4f3e423337ae3b0", + "src": "hda", + "uuid": "836c00e8-a52e-41ff-9aed-169c2737422e" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/ee864d120e6ad4da.json b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/ee864d120e6ad4da.json new file mode 100644 index 000000000..1e72e02e1 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/errors/ee864d120e6ad4da.json @@ -0,0 +1,57 @@ +{ + "model_class": "Job", + "id": "ee864d120e6ad4da", + "state": "error", + "exit_code": null, + "update_time": "2024-08-30T12:53:14.827157", + "create_time": "2024-08-30T12:53:06.972295", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", + "history_id": "156c4392fa643bca", + "external_id": "gxy-lj7sk", + "command_line": "ln -s '/galaxy/server/database/objects/c/7/7/dataset_c779310f-6c04-4ec2-a7b8-ed0679e21e17.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files' && fastqc --outdir '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files' --threads ${GALAXY_SLOTS:-2} --quiet --extract --min_length 108 --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files'/*\\.html output.html", + "traceback": null, + "params": { + "__input_ext": "\"fastqsanger\"", + "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": "8484cc763161da97", + "src": "hda", + "uuid": "c779310f-6c04-4ec2-a7b8-ed0679e21e17" + } + }, + "outputs": { + "html_file": { + "id": "3ca01b6fa3c2aaf5", + "src": "hda", + "uuid": "eff11dba-52dc-40a6-acb2-426075fb0264" + }, + "text_file": { + "id": "633d64f77bff13b3", + "src": "hda", + "uuid": "366f2433-d768-44fa-bae1-205e2035b74c" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/job-metrics.csv b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/job-metrics.csv new file mode 100644 index 000000000..325c0cddd --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/job-metrics.csv @@ -0,0 +1,95 @@ +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 +ea3e808f13e0175c,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,mummer_nucmer/4.0.0beta2+galaxy1,,,,20401.0000000,5.0000000,,,,,,1.0000000 +5835e2fe3b1be6c6,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +af686d0530be6436,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +38e5943f3cf9e7a1,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,lofreq_indelqual/2.1.5+galaxy0,,,,12240.0000000,1.0000000,,,,,,0E-7 +ba18cd8c087f0154,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +915a352ef8644fda,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,lofreq_indelqual/2.1.5+galaxy0,,,,12240.0000000,1.0000000,,,,,,0E-7 +ab2873333ea7b271,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +75468927e1e47623,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +a570955de08d43f9,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,lofreq_indelqual/2.1.5+galaxy0,,,,12240.0000000,1.0000000,,,,,,0E-7 +6438f3d32c4013c9,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +6e95eddc84cda40d,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,deeptools_bam_coverage/3.3.2.0.0,,,,25769.0000000,8.0000000,,,,,,1.0000000 +21383bfca5be1aac,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +44901ea38dea194c,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,deeptools_bam_coverage/3.3.2.0.0,,,,25769.0000000,8.0000000,,,,,,1.0000000 +0ff3cf4cdd53f073,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +7a3a784002d9b2e4,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,deeptools_bam_coverage/3.3.2.0.0,,,,25769.0000000,8.0000000,,,,,,1.0000000 +c20446b95cd50d61,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +18cc197ba26e8e47,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,deeptools_bam_coverage/3.3.2.0.0,,,,25769.0000000,8.0000000,,,,,,1.0000000 +7cf1947c1168a2c0,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +f4f3e423337ae3b0,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,deeptools_bam_coverage/3.3.2.0.0,,,,25769.0000000,8.0000000,,,,,,1.0000000 +2d284e114fa37175,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +51e554051ef9c10a,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,deeptools_bam_coverage/3.3.2.0.0,,,,25769.0000000,8.0000000,,,,,,0E-7 +fbbbf1f96f8e5488,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +e0b49637d014491c,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,deeptools_bam_coverage/3.3.2.0.0,,,,25769.0000000,8.0000000,,,,,,0E-7 +b3563ccd5e1e3ab8,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +5ea0491d7d9d49ff,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,deeptools_compute_matrix/3.3.2.0.0,,,,32212.0000000,8.0000000,,,,,,1.0000000 +b9dde3d46c4379df,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +85c44b3c6b9e7586,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +d9f9da59e3f2406f,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,deeptools_compute_matrix/3.3.2.0.0,,,,32212.0000000,8.0000000,,,,,,1.0000000 +b21d89599c6459c7,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +513a309e28516acc,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +b45576da8fb4db6c,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,deeptools_compute_matrix/3.3.2.0.0,,,,32212.0000000,8.0000000,,,,,,1.0000000 +f2e6b52237639f74,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +fcf89f603a1c7b2a,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +95658726ede0b433,156c4392fa643bca,anvil-test-2024-08-30-12-48,error,poretools_hist/0.6.1a1.1,,,,,,,,,,, +e91c490c9f6a73a2,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +4ed862dd399223fe,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,poretools_hist/0.6.1a1.1,,,,12240.0000000,1.0000000,,,,,,2.0000000 +b5fd60f450fc55cd,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +d0f64fa7dfce59dc,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,poretools_hist/0.6.1a1.1,,,,12240.0000000,1.0000000,,,,,,2.0000000 +df4be1d1e9033ceb,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +e0569ebde28ee8e6,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,vcfvcfintersect/1.0.0_rc3+galaxy0,,,,4080.0000000,1.0000000,,,,,,0E-7 +8bcd04047caac1fc,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +1a47f051541ad4a1,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +ca0dbf2286d6aab6,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +ecde87cc004b1c6a,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,vcfvcfintersect/1.0.0_rc3+galaxy0,,,,4080.0000000,1.0000000,,,,,,0E-7 +57d4cb6a07ed3fc2,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +6ba9cd0931299b66,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +57d6525ceb3c7ff6,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +849d1de06f90547b,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,vcfbedintersect/1.0.0_rc3+galaxy0,,,,4080.0000000,1.0000000,,,,,,0E-7 +7e2dda28cca230dc,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +3a9d800057b68c29,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,vcfbedintersect/1.0.0_rc3+galaxy0,,,,4080.0000000,1.0000000,,,,,,0E-7 +d7a42a5aa611aaed,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +ae94dc40a80201c8,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +a629f136fcaf7040,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,bcftools_roh/1.10,,,,4080.0000000,1.0000000,,,,,,0E-7 +a27489f36aeff263,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +5302a10e39b38a93,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,bcftools_roh/1.10,,,,4080.0000000,1.0000000,,,,,,1.0000000 +81705c8bdfb2f0c3,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +019b97a522616e6d,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,bcftools_cnv/1.10,,,,4080.0000000,1.0000000,,,,,,0E-7 +408382c4a5d7521c,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +9de808f54edb8972,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,bcftools_cnv/1.10,,,,4080.0000000,1.0000000,,,,,,4.0000000 +7eb12407ceab9b32,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +0a2d17a5e5658f2e,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,bcftools_cnv/1.10,,,,4080.0000000,1.0000000,,,,,,0E-7 +0f3b0b88fd8d3bd3,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +38e0158e5ebfa1e2,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,bcftools_cnv/1.10,,,,4080.0000000,1.0000000,,,,,,3.0000000 +7c01c4141514aa61,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +54f87b52c320e6bc,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,samtools_markdup/1.9+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +9df085a5453dfde2,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +1ba62846d1f04d18,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,samtools_markdup/1.9+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +106d1733a57037d1,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +6cded8ba9046fcf8,156c4392fa643bca,anvil-test-2024-08-30-12-48,error,samtools_markdup/1.9+galaxy2,,,,,,,,,,, +3976787d54723140,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +633d64f77bff13b3,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,samtools_markdup/1.9+galaxy2,,,,4080.0000000,1.0000000,,,,,,0E-7 +3ca01b6fa3c2aaf5,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +8484cc763161da97,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,fastqc/0.73+galaxy0,,,,32641.0000000,8.0000000,,,,,,2.0000000 +206b36d8f96e47cd,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +d21247b92014bb0d,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,fastqc/0.73+galaxy0,,,,32641.0000000,8.0000000,,,,,,3.0000000 +0fe7302a78654ddf,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +ee864d120e6ad4da,156c4392fa643bca,anvil-test-2024-08-30-12-48,error,fastqc/0.73+galaxy0,,,,,,,,,,, +c97ee8434250db99,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +af40f508fdc35ec2,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,fastqc/0.73+galaxy0,,,,32641.0000000,8.0000000,,,,,,2.0000000 +6acf2c47ca86c8b2,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +a3a4551013810557,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +f740d3c7d43bd3eb,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,fastqc/0.73+galaxy0,,,,32641.0000000,8.0000000,,,,,,2.0000000 +d3f02b5a33fb39af,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +080baf71aa6e2015,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +c47be949479cc5b9,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,fastqc/0.73+galaxy0,,,,32641.0000000,8.0000000,,,,,,3.0000000 +fa0229a69e711bff,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +6ac9981049d706dd,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +15560a63e74f84d3,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,fastqc/0.73+galaxy0,,,,32641.0000000,8.0000000,,,,,,2.0000000 +29c629bc39007a7f,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +4a8a894582b5f73d,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +9d1e1747721329c1,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,fastqc/0.73+galaxy0,,,,32641.0000000,8.0000000,,,,,,2.0000000 +e297cd7ed0a5dd6c,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +5dfc3409608a2061,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,sqlite_to_tabular/2.0.1,,,,4080.0000000,1.0000000,,,,,,0E-7 +156c4392fa643bca,156c4392fa643bca,anvil-test-2024-08-30-12-48,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 diff --git a/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/job.log b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/job.log new file mode 100644 index 000000000..ca1427043 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/job.log @@ -0,0 +1,12942 @@ +DEBUG:yacman.yacman:Patching yaml loader +DEBUG:galaxy.app:python path is: /galaxy/server/scripts, /galaxy/server/lib, /galaxy/server/lib, /usr/local/lib/python310.zip, /usr/local/lib/python3.10, /usr/local/lib/python3.10/lib-dynload, /galaxy/server/.venv/lib/python3.10/site-packages +DEBUG:galaxy.config:Configuration directory is /galaxy/server/config +DEBUG:galaxy.config:Data directory is /galaxy/server/database +DEBUG:galaxy.config:Managed config directory is /galaxy/server/config +WARNING:galaxy.config:Paths for the 'interactivetools_map' option are now relative to 'data_dir', remove the leading 'database/' to suppress this warning: database/interactivetools_map.sqlite +WARNING:galaxy.config:Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +WARNING:galaxy.config:Config option 'containers_resolvers_config_file' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file. +INFO:alembic.runtime.migration:Context impl PostgresqlImpl. +INFO:alembic.runtime.migration:Will assume transactional DDL. +INFO:galaxy.model.migrations:Your galaxy database is up-to-date +INFO:alembic.runtime.migration:Context impl PostgresqlImpl. +INFO:alembic.runtime.migration:Will assume transactional DDL. +INFO:galaxy.model.migrations:Your tool shed install database is up-to-date +INFO:galaxy.app:Install database targeting Galaxy's database configuration. +DEBUG:galaxy.web_stack:WeblessApplicationStack initialized +DEBUG:galaxy.web_stack:Will attach to pool(s): job-handlers +galaxy.jobs DEBUG 2024-08-30 12:45:59,296 [pN:job_handler_0,p:8,tN:MainThread] Read job configuration from file: /galaxy/server/config/job_conf.yml +galaxy.jobs INFO 2024-08-30 12:45:59,296 [pN:job_handler_0,p:8,tN:MainThread] Job handler assignment methods set to: db-skip-locked +galaxy.jobs INFO 2024-08-30 12:45:59,297 [pN:job_handler_0,p:8,tN:MainThread] Tag [_default_] handlers: job_handler_0 +galaxy.web_stack.handlers DEBUG 2024-08-30 12:45:59,297 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'tpv_dispatcher' +galaxy.jobs DEBUG 2024-08-30 12:45:59,297 [pN:job_handler_0,p:8,tN:MainThread] Done loading job configuration +galaxy.security.vault WARNING 2024-08-30 12:45:59,575 [pN:job_handler_0,p:8,tN:MainThread] No vault configured. We recommend defining the vault_config_file setting in galaxy.yml +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,610 [pN:job_handler_0,p:8,tN:MainThread] Loading datatypes from /galaxy/server/lib/galaxy/config/sample/datatypes_conf.xml.sample +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,610 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.h. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,610 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.c. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,611 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cpp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,611 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.py. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,611 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.go. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,611 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.rs. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,611 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cs. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,611 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hep.root. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,611 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:JP2 from the datatype registry for extension jp2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,611 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry for extension ab1. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,612 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry for extension afg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,613 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.goldenpath:GoldenPath from the datatype registry for extension agp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,613 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_cog_profile. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,613 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_composite. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,613 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension anvio_classifier. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,613 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry for extension anvio_contigs_db. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry for extension anvio_db. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry for extension anvio_genomes_db. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry for extension anvio_pan_db. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_pfam_profile. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry for extension anvio_profile_db. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry for extension anvio_samples_db. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension anvio_state. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry for extension anvio_structure_db. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension anvio_variability. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry for extension arff. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,614 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry for extension paf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry for extension gfa1. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa2 from the datatype registry for extension gfa2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension asn1. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension asn1-binary. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry for extension axt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry for extension fli. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry for extension bam. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bai. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry for extension qname_input_sorted.bam. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry for extension qname_sorted.bam. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry for extension unsorted.bam. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,615 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry for extension probam. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,616 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry for extension cram. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,616 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry for extension bed. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,616 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry for extension bedgraph. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,616 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry for extension bedstrict. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,616 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry for extension bed6. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,616 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry for extension bed12. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,616 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry for extension probed. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,616 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry for extension len. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,616 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry for extension daa. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry for extension rma6. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry for extension dmnd. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Parquet from the datatype registry for extension parquet. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry for extension idat. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry for extension bigbed. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry for extension bigwig. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cxb. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry for extension chrint. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension csv. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension tsv. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,617 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension intermine_tabular. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,618 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry for extension customtrack. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,618 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry for extension bowtie_color_index. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,618 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry for extension bowtie_base_index. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,618 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry for extension csfasta. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,618 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension data. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,618 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,618 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension binary. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,619 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension d3_hierarchy. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,619 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry for extension imgt.json. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,619 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry for extension geojson. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,619 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension data_manager_json. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,619 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry for extension dbn. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,619 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension fai. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,619 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension fasta. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,619 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry for extension fastg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,619 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry for extension fastq. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,620 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry for extension fastqsanger. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,620 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry for extension fastqsolexa. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,620 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry for extension fastqcssanger. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,620 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry for extension fastqillumina. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,620 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry for extension fqtoc. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,620 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry for extension eland. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,620 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry for extension elandmulti. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,620 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry for extension genetrack. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,620 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry for extension gff. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,621 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry for extension gff3. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,621 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry for extension gif. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,621 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry for extension gmaj.zip. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,621 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension graph_dot. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,621 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry for extension gtf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,621 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension toolshed.gz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,621 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hdf4. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,621 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,621 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension scool. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,621 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Grib from the datatype registry for extension grib. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry for extension loom. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry for extension h5ad. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Visium from the datatype registry for extension visium.tar.gz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mz5. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hyphy_results.json. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hivtrace. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry for extension cool. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry for extension mcool. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5MLM from the datatype registry for extension h5mlm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:LudwigModel from the datatype registry for extension ludwig_model. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,622 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension html. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,623 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension ludwig_report.html. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,623 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry for extension interval. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,623 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension jellyfish. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,712 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry for extension isa-tab. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,712 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry for extension isa-json. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,712 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension picard_interval_list. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,712 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_interval. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,712 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_report. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,712 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_dbsnp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,712 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_tranche. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,713 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_recal. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,713 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hhr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,713 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry for extension jpg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,713 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tiff. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,713 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,713 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf8. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,713 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension btf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,713 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tif. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension svs. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension scn. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension bif. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:OMETiff from the datatype registry for extension ome.tiff. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vms. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vmu. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension ndpi. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry for extension mrxs. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry for extension svslide. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry for extension bmp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,714 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry for extension im. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry for extension pcd. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry for extension pcx. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry for extension ppm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry for extension psd. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry for extension xbm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry for extension xpm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry for extension rgb. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry for extension pbm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry for extension pgm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nrrd. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nhdr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,715 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry for extension rna_eps. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,716 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Artifact from the datatype registry for extension qza. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,716 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Visualization from the datatype registry for extension qzv. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,716 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Metadata from the datatype registry for extension qiime2.tabular. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,716 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension zip. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,717 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension ncbi_genome_dataset.zip. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,717 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension tar. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,717 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension directory. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,717 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension yaml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,717 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mrm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,719 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta from the datatype registry for extension dta. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,719 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta2d from the datatype registry for extension dta2d. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,719 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Edta from the datatype registry for extension edta. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,719 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension pepxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,719 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension raw_pepxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,719 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension peptideprophet_pepxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,719 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension interprophet_pepxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,719 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry for extension protxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,719 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ParamXml from the datatype registry for extension paramxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,719 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Kroenik from the datatype registry for extension kroenik. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepList from the datatype registry for extension peplist. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PSMS from the datatype registry for extension psms. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry for extension pepxml.tsv. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry for extension protxml.tsv. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry for extension mascotdat. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry for extension mzid. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry for extension idxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry for extension tandem. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sirius.ms. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry for extension thermo.raw. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry for extension brukerbaf.d.tar. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry for extension agilentbrukeryep.d.tar. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry for extension brukertdf.d.tar. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,720 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry for extension agilentmasshunter.d.tar. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry for extension watersmasslynx.raw.tar. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry for extension wiff.tar. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Wiff2Tar from the datatype registry for extension wiff2.tar. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotXML from the datatype registry for extension mascotxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab from the datatype registry for extension mztab. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab2 from the datatype registry for extension mztab2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry for extension mzml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry for extension nmrml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Meryldb from the datatype registry for extension meryldb. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bref3 from the datatype registry for extension bref3. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry for extension mgf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry for extension wiff. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff2 from the datatype registry for extension wiff2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry for extension mzxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,721 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry for extension mzdata. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry for extension ms2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry for extension mzq. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry for extension sqlite. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry for extension mz.sqlite. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OSW from the datatype registry for extension osw. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PQP from the datatype registry for extension pqp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry for extension traml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TrafoXML from the datatype registry for extension trafoxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry for extension featurexml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry for extension consensusxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry for extension uniprotxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestXML from the datatype registry for extension xquest.xml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestSpecXML from the datatype registry for extension spec.xml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:QCML from the datatype registry for extension qcml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,722 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension mzqc. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry for extension msp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry for extension splib_noindex. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry for extension splib. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry for extension blib. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry for extension dlib. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry for extension elib. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry for extension hlf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry for extension idpdb. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry for extension sf3. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cps. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry for extension ct. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry for extension postgresql. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MongoDBArchive from the datatype registry for extension mongodb. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,723 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeneNoteBook from the datatype registry for extension genenotebook. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,724 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry for extension searchgui_archive. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,724 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry for extension fast5.tar. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,724 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry for extension fast5.tar.gz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,724 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry for extension fast5.tar.bz2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,724 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension peptideshaker_archive. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,724 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension percin. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,724 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension percout. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,724 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hardklor. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,724 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension kronik. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,724 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry for extension imzml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,725 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Analyze75 from the datatype registry for extension analyze75. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,725 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti1 from the datatype registry for extension nii1. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,725 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti2 from the datatype registry for extension nii2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,725 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gifti from the datatype registry for extension gii. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,725 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tck from the datatype registry for extension tck. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,725 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Trk from the datatype registry for extension trk. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,725 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mrc2014 from the datatype registry for extension mrc. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,725 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Star from the datatype registry for extension star. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,725 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PEFF from the datatype registry for extension peff. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,725 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension toml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,726 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.flow:FCS from the datatype registry for extension fcs. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,726 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowtext. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,726 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowclr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,726 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowmfi. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,726 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat1. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,727 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,727 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat3. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,727 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowscore. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,727 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowframe. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,727 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension fsom. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,727 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowset. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,727 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension metacyto_clr.txt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,728 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mSummary from the datatype registry for extension metacyto_summary.txt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,728 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mStats from the datatype registry for extension metacyto_stats.txt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,728 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_compute_matrix_archive. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,728 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_coverage_matrix. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,728 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry for extension netcdf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,728 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry for extension eps. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,728 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry for extension rast. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,728 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry for extension laj. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,728 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry for extension lav. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,728 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry for extension maf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry for extension mafcustomtrack. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry for extension mtx. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CMAP from the datatype registry for extension cmap. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry for extension encodepeak. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry for extension pdf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry for extension pileup. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Psl from the datatype registry for extension psl. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry for extension obo. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry for extension owl. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry for extension png. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry for extension qual. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,729 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry for extension qualsolexa. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry for extension qualillumina. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry for extension qualsolid. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry for extension qual454. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry for extension roadmaps. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry for extension sam. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry for extension scf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry for extension sequences. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry for extension snpeffdb. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry for extension snpsiftdbnsfp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dbnsfp.tabular. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry for extension sff. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry for extension sra. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,730 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:SraManifest from the datatype registry for extension sra_manifest.tabular. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,731 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension svg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,731 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry for extension taxonomy. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,731 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension tabular. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,731 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry for extension twobit. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,731 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQmass from the datatype registry for extension sqmass. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,731 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry for extension gemini.sqlite. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,731 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ChiraSQLite from the datatype registry for extension chira.sqlite. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,731 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry for extension cuffdiff.sqlite. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,731 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry for extension gafa.sqlite. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,731 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NcbiTaxonomySQlite from the datatype registry for extension ncbitaxonomy.sqlite. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension txt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry for extension linecount. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry for extension memepsp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry for extension memexml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry for extension cisml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xsd. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Dzi from the datatype registry for extension dzi. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry for extension vcf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf_bgzip. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry for extension bcf_uncompressed. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,732 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry for extension velvet. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,733 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry for extension wig. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,733 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension interval_index. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,733 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension odgi. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,733 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension vg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,733 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension xg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,733 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,733 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf3. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,733 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension onnx. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,733 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tabix. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:IntervalTabix from the datatype registry for extension interval_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:JuicerMediumTabix from the datatype registry for extension juicer_medium_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedTabix from the datatype registry for extension bed_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:GffTabix from the datatype registry for extension gff_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bgzip. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry for extension vcf_bgzip. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bus. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension kallisto.idx. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry for extension phyloxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension newick. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,734 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension nhx. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,735 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry for extension nex. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,735 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry for extension iqtree. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,736 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mldist. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,739 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry for extension affybatch. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,739 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry for extension eigenstratgeno. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,739 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry for extension eigenstratpca. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry for extension eset. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry for extension fped. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry for extension fphe. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry for extension gg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry for extension ldindep. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry for extension malist. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry for extension lped. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry for extension pbed. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry for extension pheno. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry for extension pphe. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry for extension rexpbase. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,740 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry for extension rgenetics. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,741 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry for extension snptest. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,741 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry for extension snpmatrix. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,741 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension xls. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,741 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry for extension ipynb. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,741 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension json. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,741 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry for extension expression.json. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,742 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry for extension xgmml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,742 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry for extension sif. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,743 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry for extension triples. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,743 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry for extension hdt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,743 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry for extension nt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,743 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry for extension n3. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,743 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry for extension ttl. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,743 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry for extension rdf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,743 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry for extension jsonld. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,743 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension excel.xls. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,744 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry for extension xlsx. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,744 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension btwisted. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,744 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cai. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,744 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cat_db. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,744 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension charge. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,744 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension checktrans. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,744 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension chips. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,744 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codcmp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,744 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension coderet. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,744 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension compseq. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgplot. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgreport. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cusp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cut. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dan. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension digest. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dreg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension einverted. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension epestfind. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension equicktandem. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,745 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension est2genome. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,746 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension etandem. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,746 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension freak. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,746 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzznuc. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,746 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzzpro. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,746 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzztran. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,746 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension garnier. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,746 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension geecee. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,746 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension helixturnhelix. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,746 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hmoment. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,746 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension isochore. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,747 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension match. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,747 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nametable. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,747 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension needle. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,747 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgreport. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,747 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgseek. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,747 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension noreturn. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,747 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension palindrome. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,747 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepcoil. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,747 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepinfo. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,747 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepstats. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension polydot. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension preg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prettyseq. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension primersearch. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showfeat. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showorf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sixpack. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension strider. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension supermatcher. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension syco. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,748 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension textsearch. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension vectorstrip. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wobble. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wordcount. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dbmotif. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension diffseq. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension excel. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feattable. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension motif. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension regions. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension seqtable. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension simple. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,749 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension table. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,750 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension tagseq. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,750 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension acedb. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,750 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension clustal. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,750 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codata. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,750 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension embl. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,750 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fitch. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,750 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gcg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,750 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry for extension genbank. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,750 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hennig86. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,751 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ig. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,751 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifer. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,751 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifernon. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,751 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mega. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,751 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension meganon. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,751 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ncbi. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,751 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexus. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,751 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexusnon. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,752 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry for extension phylip. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,752 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension phylipnon. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,752 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pir. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,752 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension staden. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,752 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension swiss. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,753 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Msf from the datatype registry for extension msf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,753 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx0. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,753 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx1. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,754 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx10. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,754 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,754 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx3. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,754 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pair. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,754 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension score. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,754 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srs. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,754 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srspair. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,755 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry for extension snaphmm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,755 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry for extension augustus. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,755 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry for extension icm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,755 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry for extension cm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,755 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry for extension hmm2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,755 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry for extension hmm3. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,755 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry for extension stockholm. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,755 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry for extension xmfa. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,756 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry for extension cel. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,756 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry for extension gpr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,756 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry for extension gal. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,756 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension rds. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,756 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension phyloseq. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,756 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,756 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.sce. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,757 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.raw. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,757 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.msnbase.raw. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,757 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.findchrompeaks. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,757 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.group. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,757 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.retcor. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,757 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.fillpeaks. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,757 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.positive. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,757 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.negative. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,757 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.quick. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,758 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.hdf5:HDF5SummarizedExperiment from the datatype registry for extension rdata.se. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,758 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rdock_as. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,758 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry for extension oxlicg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,758 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry for extension oxling. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,758 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry for extension oxlits. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,758 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry for extension oxlist. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,758 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry for extension oxliss. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,758 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry for extension oxligl. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,759 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry for extension stl. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,760 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry for extension plyascii. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,760 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry for extension plybinary. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,760 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry for extension vtkascii. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,760 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry for extension vtkbinary. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,760 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry for extension biom1. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,760 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry for extension biom2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,760 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry for extension msh. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,760 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry for extension scidx. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,762 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry for extension smi. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,762 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry for extension sdf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,762 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry for extension inchi. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,762 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry for extension mol. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,762 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry for extension mol2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,762 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry for extension cml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,762 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry for extension fps. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,762 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry for extension obfs. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry for extension drf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry for extension phar. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry for extension pdb. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry for extension pdbqt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry for extension pqr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Cell from the datatype registry for extension cell. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CIF from the datatype registry for extension cif. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:XYZ from the datatype registry for extension xyz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:ExtendedXYZ from the datatype registry for extension extxyz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry for extension trr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry for extension dcd. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,763 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension top. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,764 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prmtop. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,764 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension itp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,764 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mdp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,764 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ndx. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,764 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension xvg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,764 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry for extension xtc. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,764 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry for extension cpt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,764 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry for extension edr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,764 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tpr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,765 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:GRO from the datatype registry for extension gro. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,765 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension inpcrd. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,765 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry for extension vel. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,765 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry for extension grd. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,765 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry for extension grd.tgz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,765 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.otu. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,765 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.list. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,765 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.sabund. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,765 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.rabund. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,765 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.shared. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,766 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.relabund. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,766 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry for extension mothur.names. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,766 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.design. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,766 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry for extension mothur.summary. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,766 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.groups. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,766 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry for extension mothur.oligos. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,766 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension mothur.align. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,766 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.accnos. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,766 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.otulabels. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,767 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mothur.otu.corr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,767 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry for extension mothur.map. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,767 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry for extension mothur.align.check. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,767 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry for extension mothur.align.report. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,767 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry for extension mothur.filter. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,767 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry for extension mothur.dist. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,767 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mothur.tre. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,767 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry for extension mothur.pair.dist. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,767 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mothur.square.dist. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,768 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry for extension mothur.lower.dist. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,768 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.ref.taxonomy. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,768 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.seq.taxonomy. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,768 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.rdp.taxonomy. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,768 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry for extension mothur.cons.taxonomy. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,768 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry for extension mothur.tax.summary. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,768 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry for extension mothur.freq. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,768 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.quan. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,768 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.quan. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,769 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.masked.quan. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,769 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.masked.quan. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,769 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry for extension mothur.axes. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,769 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry for extension mothur.sff.flow. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,769 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry for extension mothur.count_table. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,770 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry for extension neostore. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,770 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry for extension neostore.zip. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,770 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry for extension trackhub. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,771 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry for extension blastxml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,771 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry for extension blastdbn. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,771 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry for extension blastdbp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,771 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry for extension blastdbd. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,771 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:LastDb from the datatype registry for extension lastdb. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,771 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb5 from the datatype registry for extension blastdbn5. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,771 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb5 from the datatype registry for extension blastdbp5. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,772 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb5 from the datatype registry for extension blastdbd5. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,772 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension maskinfo-asn1. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,772 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension maskinfo-asn1-binary. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,772 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension pssm-asn1. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,772 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry for extension ptkscmp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,773 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry for extension smat. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,773 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry for extension alohomora_gts. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,773 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_map. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,773 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_maf. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,773 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_ped. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,773 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension linkage_pedin. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,773 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry for extension linkage_datain. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,773 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry for extension linkage_map. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,773 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_ihaplo. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,774 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_descent. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,774 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry for extension allegro_fparam. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,774 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry for extension ideaspre. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,774 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry for extension sbml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,774 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry for extension spalndbnp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,775 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry for extension spalndba. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,775 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_dada. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,775 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_errorrates. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,775 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_mergepairs. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,775 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_sequencetable. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,775 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_uniques. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,775 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension ampvis2. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,775 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ckpt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,776 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tgz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,782 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wav from the datatype registry for extension wav. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,782 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp3 from the datatype registry for extension mp3. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,782 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mkv from the datatype registry for extension mkv. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,782 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp4 from the datatype registry for extension mp4. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,782 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Flv from the datatype registry for extension flv. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,782 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mpg from the datatype registry for extension mpg. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,783 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:TextGrid from the datatype registry for extension textgrid. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,783 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:BPF from the datatype registry for extension par. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,783 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension ffindex. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,783 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension ffdata. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,783 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Pretext from the datatype registry for extension pretext. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,783 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension immuneml_receptors.html. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,783 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdMaterials from the datatype registry for extension hexrd.materials.h5. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,784 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension npz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,784 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdImagesNpz from the datatype registry for extension hexrd.images.npz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,784 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdEtaOmeNpz from the datatype registry for extension hexrd.eta_ome.npz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,784 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension hexrd.scored_orientations.npz. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,784 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hexrd.accepted_orientations. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,784 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension hexrd.yml. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,784 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTess from the datatype registry for extension neper.tess. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,784 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTesr from the datatype registry for extension neper.tesr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,784 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPoints from the datatype registry for extension neper.points. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,784 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular from the datatype registry for extension neper.points.tsv. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell from the datatype registry for extension neper.mscell. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshMsh from the datatype registry for extension gmsh.msh. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshGeo from the datatype registry for extension gmsh.geo. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:ZsetGeof from the datatype registry for extension zset.geof. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension pov. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaResult from the datatype registry for extension pithya.result. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaProperty from the datatype registry for extension pithya.property. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaModel from the datatype registry for extension pithya.model. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLts from the datatype registry for extension bcsl.ts. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLmodel from the datatype registry for extension bcsl.model. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormSample from the datatype registry for extension storm.sample. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormCheck from the datatype registry for extension storm.check. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:CTLresult from the datatype registry for extension ctl.result. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,785 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Castep from the datatype registry for extension castep. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,786 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Param from the datatype registry for extension param. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,786 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:FormattedDensity from the datatype registry for extension den_fmt. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,786 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bil. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,786 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hdr. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,786 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry for extension shp. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,786 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:FITS from the datatype registry for extension fits. +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2024-08-30 12:45:59,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,114 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Html' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,119 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,120 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Star' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,121 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Param' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,122 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,123 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,123 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,123 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,123 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,123 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,127 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ucsc': /cvmfs/data.galaxyproject.org/managed/location/ucsc_build_sites.txt with display sites: ['main', 'archaea', 'ucla'] +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,128 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'gbrowse': /galaxy/server/tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['wormbase', 'tair', 'modencode_worm', 'modencode_fly'] +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,128 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ensembl': /galaxy/server/tool-data/shared/ensembl/ensembl_sites.txt +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,128 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ensembl_data_url': /galaxy/server/tool-data/shared/ensembl/ensembl_sites_data_URL.txt +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,128 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'igv': /galaxy/server/tool-data/shared/igv/igv_build_sites.txt.sample +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:00,128 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'rviewer': /galaxy/server/tool-data/shared/rviewer/rviewer_build_sites.txt.sample +galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-08-30 12:46:00,129 [pN:job_handler_0,p:8,tN:MainThread] Loading references to tool sheds from internal default config +galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-08-30 12:46:00,129 [pN:job_handler_0,p:8,tN:MainThread] Loaded reference to tool shed: Galaxy Main Tool Shed +galaxy.web_stack DEBUG 2024-08-30 12:46:00,130 [pN:job_handler_0,p:8,tN:MainThread] server_name set to: job_handler_0 +galaxy.queue_worker INFO 2024-08-30 12:46:00,135 [pN:job_handler_0,p:8,tN:MainThread] Initializing job_handler_0 Galaxy Queue Worker on amqp://default_user_H1uS_mJCApRV-OafvJx:********@prod-24-08-30-12-32-1-galaxy-rabbitmq-server:5672 +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,151 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/db536ad45f28/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,151 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,152 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ee2beb764a7b/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,152 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,152 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/78bbd17d0703/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,152 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,152 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/7fe36019c073/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,152 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,152 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/2cf4a1cafc16/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,152 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/f95f403841ad/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/d6dc477167f8/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/672b6c02fbc7/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/365325116147/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/fec517907949/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,153 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/c077f71d351f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/ed4ea9de1791/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/dfef7a353ed0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/01d6b7d6365e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/8abfcd1a6949/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/4813f99d81b7/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,154 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/0dbff46d5a1b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bf235558f2cf/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/d40d4bf05718/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/b8e9da766b0f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/776ad0b21536/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,155 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/9ef52d95114b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/b17394940c7a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/582f8b13873d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bf7d6acd9884/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/02f349bdbf96/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/e03f2f3ac3a9/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,156 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,157 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/b76adb2f1c51/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,157 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,157 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/072f606e2e69/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,157 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,157 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/23680a42e149/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,157 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,157 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/6ca7c55a27e8/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,157 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/fdd127bd4a32/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/403553ae19f6/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/5c232a738c74/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/c9c5718edc19/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bdfdf5f6e950/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/2968c6916579/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,158 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/a3dea556218d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/29f9b782727e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/17096387c0e6/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/166c4f50525f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,159 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/all_gff.loc' for tool data table 'all_gff' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'all_gff' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/dbkeys.loc' for tool data table '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table '__dbkeys__' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/093678460093/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "all_fasta", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,160 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,161 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/4542035c1075/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,161 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,161 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/minimap2/f54f5baedfdd/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,161 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,161 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/09b2cdb7ace5/bowtie2_indices.loc' for tool data table 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,161 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,161 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/3fe632431b68/bwa_mem_index.loc' for tool data table 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,161 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_mem_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,162 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bwameth/29bdbc353f20/bwameth_indexes.loc' for tool data table 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,162 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwameth_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,162 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/lastz/e7f19d6a9af8/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,162 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,162 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/43815fa60f3a/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,162 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,163 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/a7228a7ea146/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,163 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,163 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/336b3def9b2b/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,163 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,163 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/db25ec99c3ea/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,163 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,163 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmon/cc05793bb896/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,163 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,163 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/a8f343909c17/sailfish_indexes.loc' for tool data table 'sailfish_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'sailfish_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/26371a1df031/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/stringtie/1ebd14235b92/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/b72793637686/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/a3b4ad6858ff/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/4d343c1f606b/sam_fa_indices.loc' for tool data table 'sam_fa_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,164 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'sam_fa_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/145f6d74ff5e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/06dc50b7b711/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/fa7ad9b89f4a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/cf1ffd88f895/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/e1461b5c52a0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/aa35ee7f3ab2/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,165 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/426d707dfc47/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/7dfca164d2e3/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/09d6e4693887/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/ef2c525bd8cd/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/d12a810c837e/snpeff_msigdb_database.loc' for tool data table 'snpeff_msigdb_database' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeff_msigdb_database' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,166 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/4e21e4f2bc48/snpsift_dbnsfps.loc' for tool data table 'snpsift_dbnsfps' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpsift_dbnsfps' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/74aebe30fb52/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/74aebe30fb52/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/2b62154e39c8/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/alevin/e4c01dcece8b/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,167 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/88c07fc4024c/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/093678460093/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/c772497b2c32/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/eec9494fdafa/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,168 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/38b6d12edc68/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/38b6d12edc68/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/alevin/ecb9ea6269ee/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/2055c2667eb3/rnastar_index2.loc' for tool data table 'rnastar_index2' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rnastar_index2' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f3a5f075498f/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f3a5f075498f/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,169 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/24c5d43cb545/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/all_gff.loc' for tool data table 'all_gff' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_gff' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/dbkeys.loc' for tool data table '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/135b80fb1ac2/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/980d2a2e1180/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,170 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/b502c227b5e6/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/f4af63aaf57a/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c5e2e5902201/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/660cffd8d92a/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/e3ba567abdf5/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/e3ba567abdf5/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,171 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/f088370d2a3c/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/f088370d2a3c/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/e188dc7a68e6/bwa_mem_index.loc' for tool data table 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/a1f0b3f4b781/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/b9fbec5ac6b2/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,172 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/61ee47027bd3/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/1759d845181e/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/1759d845181e/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/d080005cffe1/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/5826298f6a73/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/0dbf49c414ae/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,173 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/4805fe3d8fda/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/65432c3abf6c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/2270a8b83c12/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/cf61daf064fe/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/c2a413e47fe9/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,174 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/4c5f4e9b1931/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/77a1e60fd1de/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/666f60a9331a/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/a5937157062f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/156b60c1530f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/5b80f544c67f/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,175 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,176 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/5b80f544c67f/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,176 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,176 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/68693743661e/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,176 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,176 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/68693743661e/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,176 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,178 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta_dbkeys.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,178 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,179 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,179 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,180 [pN:job_handler_0,p:8,tN:MainThread] Loaded 18 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,181 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,182 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/alignseq.loc' for 'alignseq_seq' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,182 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'alignseq_seq' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,183 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,183 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'twobit' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,184 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,184 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,186 [pN:job_handler_0,p:8,tN:MainThread] Loaded 35 lines from '/cvmfs/data.galaxyproject.org/managed/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,186 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,187 [pN:job_handler_0,p:8,tN:MainThread] Loaded 35 lines from '/cvmfs/data.galaxyproject.org/managed/location/tophat2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,187 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,188 [pN:job_handler_0,p:8,tN:MainThread] Loaded 59 lines from '/cvmfs/data.galaxyproject.org/managed/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,189 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,189 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['ce9', 'ce9', 'C. elegans (WS210): ce9', '/cvmfs/data.galaxyproject.org/managed/hisat2_index/ce9/ce9']) to data table 'hisat2_indexes', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,191 [pN:job_handler_0,p:8,tN:MainThread] Loaded 47 lines from '/cvmfs/data.galaxyproject.org/managed/location/bwa_mem_index.loc' for 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,191 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,191 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['papHam1', 'papHam1', 'Baboon (Papio anubis): papHam1', '/cvmfs/data.galaxyproject.org/managed/bwa_mem_index/papHam1/papHam1.fa']) to data table 'bwa_mem_indexes', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,192 [pN:job_handler_0,p:8,tN:MainThread] Loaded 20 lines from '/cvmfs/data.galaxyproject.org/managed/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,192 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,193 [pN:job_handler_0,p:8,tN:MainThread] Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/picard_index.loc' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,194 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,194 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken_databases.loc' for 'kraken_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,195 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'kraken_databases' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,196 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,196 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_taxonomy' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,201 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1193 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys_ucsc.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,202 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,231 [pN:job_handler_0,p:8,tN:MainThread] Loaded 14 lines from '/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2.loc' for 'rnastar_index2' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,232 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,233 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/managed/location/plant_tribes_scaffolds.loc' for 'plant_tribes_scaffolds' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,233 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'plant_tribes_scaffolds' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,234 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/maf_indexes.loc' for 'maf_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,234 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'maf_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,235 [pN:job_handler_0,p:8,tN:MainThread] Loaded 15 lines from '/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,236 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,237 [pN:job_handler_0,p:8,tN:MainThread] Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken2_databases.loc' for 'kraken2_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,237 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'kraken2_databases' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,240 [pN:job_handler_0,p:8,tN:MainThread] Loaded 237 lines from '/cvmfs/data.galaxyproject.org/byhand/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,240 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,242 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['ornAna1', 'ornAna1', 'Platypus (Ornithorhynchus anatinus): ornAna1', '/cvmfs/data.galaxyproject.org/byhand/ornAna1/seq/ornAna1.fa']) to data table 'all_fasta', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,244 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dbkeys.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,244 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,245 [pN:job_handler_0,p:8,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bfast_indexes.loc' for 'bfast_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,245 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bfast_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,246 [pN:job_handler_0,p:8,tN:MainThread] Loaded 6 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb.loc' for 'blastdb' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,246 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,247 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb_p.loc' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,247 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb_p' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,249 [pN:job_handler_0,p:8,tN:MainThread] Loaded 122 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,249 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,250 [pN:job_handler_0,p:8,tN:MainThread] Loaded 16 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_mem_index.loc' for 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,251 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,252 [pN:job_handler_0,p:8,tN:MainThread] Loaded 201 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_index.loc' for 'bwa_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,252 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,253 [pN:job_handler_0,p:8,tN:MainThread] Loaded 9 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_index_color.loc' for 'bwa_indexes_color' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,254 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,255 [pN:job_handler_0,p:8,tN:MainThread] Loaded 24 lines from '/cvmfs/data.galaxyproject.org/byhand/location/maf_index.loc' for 'indexed_maf_files' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,255 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'indexed_maf_files' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,256 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ngs_sim_fasta.loc' for 'ngs_sim_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,256 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ngs_sim_fasta' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,257 [pN:job_handler_0,p:8,tN:MainThread] Loaded 10 lines from '/cvmfs/data.galaxyproject.org/byhand/location/perm_base_index.loc' for 'perm_base_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,257 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'perm_base_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,258 [pN:job_handler_0,p:8,tN:MainThread] Loaded 10 lines from '/cvmfs/data.galaxyproject.org/byhand/location/perm_color_index.loc' for 'perm_color_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,258 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'perm_color_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,259 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/picard_index.loc' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,259 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,261 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/gatk_sorted_picard_index.loc' for 'gatk_picard_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,261 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gatk_picard_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,261 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/cvmfs/data.galaxyproject.org/byhand/location/gatk_annotations.txt' for tool data table 'gatk_annotations' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,261 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gatk_annotations' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,263 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/picard_index.loc' for 'srma_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,263 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'srma_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,265 [pN:job_handler_0,p:8,tN:MainThread] Loaded 202 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'tophat_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,265 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,267 [pN:job_handler_0,p:8,tN:MainThread] Loaded 194 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices_color.loc' for 'tophat_indexes_color' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,267 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,268 [pN:job_handler_0,p:8,tN:MainThread] Loaded 122 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,268 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'tophat2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,270 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ccat_configurations.loc' for 'ccat_configurations' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,270 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ccat_configurations' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,272 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mosaik_index.loc' for 'mosaik_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,272 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mosaik_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,276 [pN:job_handler_0,p:8,tN:MainThread] Loaded 202 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'bowtie_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,276 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,278 [pN:job_handler_0,p:8,tN:MainThread] Loaded 194 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices_color.loc' for 'bowtie_indexes_color' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,278 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,280 [pN:job_handler_0,p:8,tN:MainThread] Loaded 192 lines from '/cvmfs/data.galaxyproject.org/byhand/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,280 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,283 [pN:job_handler_0,p:8,tN:MainThread] Loaded 180 lines from '/cvmfs/data.galaxyproject.org/byhand/location/sam_fa_indices.loc' for 'sam_fa_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,283 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'sam_fa_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,287 [pN:job_handler_0,p:8,tN:MainThread] Loaded 177 lines from '/cvmfs/data.galaxyproject.org/byhand/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,287 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1181 lines from '/cvmfs/data.galaxyproject.org/byhand/location/liftOver.loc' for 'liftOver' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'liftOver' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded 25 lines from '/cvmfs/data.galaxyproject.org/byhand/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,294 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'twobit' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded 106 lines from '/cvmfs/data.galaxyproject.org/byhand/location/customProDB.loc' for 'customProDB' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'customProDB' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,297 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,298 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,298 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,299 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/snpeffv_genomedb.loc' for 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,299 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,299 [pN:job_handler_0,p:8,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwameth_indexes.loc' for 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,300 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwameth_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,301 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/metaphlan_database_versioned.loc' for 'metaphlan_database_versioned' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,301 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'metaphlan_database_versioned' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,302 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/busco_database.loc' for 'busco_database' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,302 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'busco_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,303 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_config.tsv' for 'ncbi_fcs_gx_config' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,303 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_config' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,304 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_databases.loc' for 'ncbi_fcs_gx_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,305 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,306 [pN:job_handler_0,p:8,tN:MainThread] Loaded 63 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_divisions.tsv' for 'ncbi_fcs_gx_divisions' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,306 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_divisions' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,307 [pN:job_handler_0,p:8,tN:MainThread] Loaded 8 lines from '/cvmfs/data.galaxyproject.org/byhand/location/rRNA_databases.loc' for 'rRNA_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,307 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rRNA_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,309 [pN:job_handler_0,p:8,tN:MainThread] Loaded 6 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mitos.loc' for 'mitos' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,309 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mitos' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,310 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dada2_species.loc' for 'dada2_species' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,310 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'dada2_species' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,311 [pN:job_handler_0,p:8,tN:MainThread] Loaded 9 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dada2_taxonomy.loc' for 'dada2_taxonomy' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,311 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'dada2_taxonomy' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,313 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mapseq_db.loc' for 'mapseq_db' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,313 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mapseq_db' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,314 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bracken_databases.loc' for 'bracken_databases' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,314 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bracken_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,315 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/plasmidfinder_database.loc' for 'plasmidfinder_database' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,315 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'plasmidfinder_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,317 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/amrfinderplus.loc' for 'amrfinderplus_database' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,317 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'amrfinderplus_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,318 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/amrfinderplus_versioned.loc' for 'amrfinderplus_versioned_database' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,318 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'amrfinderplus_versioned_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,320 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bakta_database.loc' for 'bakta_database' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,320 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bakta_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,322 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,322 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'ncbi_taxonomy' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,326 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/all_fasta.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,328 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/all_fasta.loc.sample' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,328 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,329 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/bfast_indexes.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,331 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,331 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bfast_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,331 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bfast_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,332 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,334 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb.loc.sample' for 'blastdb' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,334 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'blastdb' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,334 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "blastdb", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,335 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb_p.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,336 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb_p.loc.sample' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,336 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'blastdb_p' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,336 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "blastdb_p", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,336 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb_d.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,338 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb_d.loc.sample' for 'blastdb_d' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,338 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb_d' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,339 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,339 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,339 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bwa_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,340 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,340 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_indexes_color' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,340 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bwa_indexes_color", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,340 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/maf_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,341 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/maf_index.loc.sample' for 'indexed_maf_files' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,342 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'indexed_maf_files' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,342 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/ngs_sim_fasta.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,343 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,343 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'ngs_sim_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,343 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "ngs_sim_fasta", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,344 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/perm_base_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,346 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,346 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'perm_base_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,346 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "perm_base_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,347 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/perm_color_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,349 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,349 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'perm_color_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,349 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "perm_color_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,350 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/picard_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,351 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/picard_index.loc.sample' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,351 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,351 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "picard_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,352 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/picard_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,353 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/picard_index.loc.sample' for 'srma_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,353 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'srma_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,353 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "srma_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,354 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/mosaik_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,355 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,355 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'mosaik_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,355 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "mosaik_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,356 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/twobit.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,358 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/twobit.loc.sample' for 'twobit' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,358 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'twobit' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,358 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "twobit", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +charset_normalizer DEBUG 2024-08-30 12:46:00,509 [pN:job_handler_0,p:8,tN:MainThread] Encoding detection: utf_8 is most likely the one. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,510 [pN:job_handler_0,p:8,tN:MainThread] Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-kdykonph". +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,515 [pN:job_handler_0,p:8,tN:MainThread] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): + +galaxy.tool_util.data WARNING 2024-08-30 12:46:00,515 [pN:job_handler_0,p:8,tN:MainThread] Line 2 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): +AccessDeniedAccess DeniedC26B0HN2GVWN41AEJO0k7Tg03ImE6EC7geV0UhkAO5gU0lPOMRmANSL01If8aPhY9nEcP4lKpUfgsQAuetn7KCvPAnc= +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-kdykonph' for 'igv_broad_genomes' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'igv_broad_genomes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-08-30 12:46:00,518 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/liftOver.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/liftOver.loc.sample' for 'liftOver' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,519 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'liftOver' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,520 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "liftOver", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,521 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/bam_iobio.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/bam_iobio.loc.sample' for 'bam_iobio' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bam_iobio' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-08-30 12:46:00,523 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/vcf_iobio.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'vcf_iobio' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-08-30 12:46:00,525 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/biom_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'biom_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-08-30 12:46:00,527 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/intermine_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/intermine_simple_display.loc.sample' for 'intermine_simple_display' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'intermine_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-08-30 12:46:00,529 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/icn3d_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/icn3d_simple_display.loc.sample' for 'icn3d_simple_display' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'icn3d_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,530 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table '__dbkeys__'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,531 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table '__dbkeys__'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,531 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,531 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'all_fasta'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,531 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'all_fasta'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,531 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,531 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'fasta_indexes'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,531 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'fasta_indexes'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,531 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,532 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bowtie2_indexes'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,532 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bowtie2_indexes'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,532 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,532 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bwa_mem_indexes'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,532 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bwa_mem_indexes'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,532 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,532 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'hisat2_indexes'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,532 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'hisat2_indexes'. +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,532 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-08-30 12:46:00,533 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/q2view_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/q2view_display.loc.sample' for 'q2view_display' +galaxy.tool_util.data DEBUG 2024-08-30 12:46:00,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'q2view_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.util.dbkeys ERROR 2024-08-30 12:46:00,535 [pN:job_handler_0,p:8,tN:MainThread] ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy/server/database/tool-data/\n/cvmfs/data.galaxyproject.org/managed/location/builds.txt' +galaxy.util WARNING 2024-08-30 12:46:00,612 [pN:job_handler_0,p:8,tN:MainThread] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2024-08-30 12:46:00,619 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:46:00,619 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:00,619 [pN:job_handler_0,p:8,tN:MainThread] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:46:00,670 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:46:00,670 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:46:00,863 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:46:00,863 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:46:00,867 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 865, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1092, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 530, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 546, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 802, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 799, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1123, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1414, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1622, in parse_param_elem + param = ToolParameter.build(self, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 319, in build + return parameter_types[param_type](tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2044, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1832, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 178, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 50, in from_element + return validator_types[_type].from_element(param, elem) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 727, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-08-30 12:46:00,908 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:46:00,909 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:00,920 [pN:job_handler_0,p:8,tN:MainThread] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:00,922 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_trim' from owner 'iuc' was not found in database. Tool will be loaded without install database. +sqlitedict DEBUG 2024-08-30 12:46:00,923 [pN:job_handler_0,p:8,tN:MainThread] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite' +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:00,941 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_removereads' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:00,946 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff_sars_cov_2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:00,955 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:00,961 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_filtervariants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:00,967 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_getmasked' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:00,973 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_variants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:00,979 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:00,987 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_gtcheck' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:00,994 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fixploidy' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,002 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_to_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,009 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_norm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,018 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query_list_samples' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,024 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_missing2ref' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,033 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_cnv' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,044 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_setgt' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,053 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_counts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,060 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_mpileup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,071 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_mendelian' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,080 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_concat' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,088 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_from_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,099 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_impute_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,107 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_reheader' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,115 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_stats' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,126 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_an_ac' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,135 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_tags' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,144 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_isec' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,152 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,160 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_roh' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,169 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,180 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,190 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,199 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_csq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,207 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_annotate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,216 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_dosage' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,224 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,234 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_tag2tag' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,243 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcf2tsv' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,251 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfaddinfo' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,257 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfallelicprimitives' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,264 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfannotate' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,270 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfannotategenotypes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,278 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfbedintersect' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,285 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfbreakcreatemulti' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,294 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcheck' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,301 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcombine' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,307 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcommonsamples' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,313 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcffixup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,320 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfflatten' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,326 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfgeno2haplo' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,334 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfgenotypes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,342 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfhethom' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,348 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfleftalign' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,356 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfprimers' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,363 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfrandomsample' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,371 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfsort' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,379 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfvcfintersect' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,388 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfselectsamples' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,396 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfdistance' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,402 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcffilter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,409 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfdistance' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,416 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcftools_annotate' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,422 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcftools_slice' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,428 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfallelicprimitives' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,435 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bedtools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,655 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bedtools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,867 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collapse_collections' from owner 'nml' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,874 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_to_collection' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,885 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collection_element_identifiers' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,890 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collection_column_join' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,896 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_matrix' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,905 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_heatmap' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,914 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,924 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_pe_fragmentsize' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,932 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bigwig_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,938 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,945 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_correct_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,952 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bam_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,960 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bigwig_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,969 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_correlation' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,978 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,988 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_enrichment' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:01,996 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_fingerprint' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,005 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_pca' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,012 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,022 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_profile' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,030 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,044 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,054 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,062 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trimmomatic' from owner 'pjbriggs' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,070 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,086 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,095 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,107 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,120 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,133 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,145 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,154 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,163 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,185 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ncbi_acc_download' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,192 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,214 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pygenometracks' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,241 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'circos' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,317 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jbrowse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.sanitize DEBUG 2024-08-30 12:46:02,335 [pN:job_handler_0,p:8,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,344 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'volcanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,351 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jbrowse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.sanitize DEBUG 2024-08-30 12:46:02,369 [pN:job_handler_0,p:8,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,377 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pathview' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,385 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pathview' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,391 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,398 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,405 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,411 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'volcanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,418 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'minimap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,429 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bowtie2' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,445 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwa' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,465 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwameth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,472 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lastz' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,490 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,505 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rna_starsolo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,520 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,533 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,550 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwa' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,570 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_nucmer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,577 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummerplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,585 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_show_coords' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,591 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_dnadiff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,598 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,606 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_delta_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,613 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,620 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flye' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,628 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,634 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,641 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,646 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'nanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,655 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_events' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,660 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_hist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,667 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_occupancy' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,673 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_qualpos' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,679 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_squiggle' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,685 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_yield_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,693 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'porechop' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,702 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_winner' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,708 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_times' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,714 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,720 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_stats' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,726 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_qualdist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,731 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_nucdist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,738 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,745 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-08-30 12:46:02,753 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fa', which is used in the 'format' attribute of parameter 'transcript' +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,757 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_pseudo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,765 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_quant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,772 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,781 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,793 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'edger' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,804 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sailfish' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,812 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,829 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'stringtie' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,844 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,853 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,865 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,878 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,896 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,906 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,922 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,933 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cufflinks' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,945 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deg_annotate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,952 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'goseq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,965 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'goseq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,975 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,987 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:02,997 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'egsea' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,007 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fgsea' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,015 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rseqc' from owner 'nilesh' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,166 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rseqc' from owner 'nilesh' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,306 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pileup_interval' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,312 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,321 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,334 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_reheader' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,341 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_pileup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,348 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,356 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,364 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam2interval' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,370 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_multi_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,378 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_phase' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,386 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,394 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_markdup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,400 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fixmate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,406 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fastx' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,416 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_depth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,425 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_stats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,434 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,440 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_bedcov' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,448 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_calmd' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,456 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,463 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtool_filter2' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,471 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_flagstat' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,477 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_sort' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,486 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_mpileup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,496 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bam_to_sam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,503 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,515 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_to_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,521 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_slice_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,529 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_rmdup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,534 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'filter_on_md' from owner 'boris' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,540 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_merge' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,546 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_stats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,554 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_phase' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,561 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,569 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_markdup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,577 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,583 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,590 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,602 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,614 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,620 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'revertr2orientationinbam' from owner 'lldelisle' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,625 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'filter_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,633 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'query_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,646 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_maker' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,652 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sqlite_to_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,659 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,667 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'concatenate_multiple_datasets' from owner 'mvdbeek' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,673 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'regex_find_replace' from owner 'galaxyp' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:03,686 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'table_compute' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,009 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_on_column' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,017 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'add_input_name_as_column' from owner 'mvdbeek' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,022 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,128 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'reshape2_melt' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,134 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'reshape2_cast' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,139 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,144 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gff3_rebase' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,151 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_remove_by_header' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,157 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_order_header_sort' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,163 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'replace_column_by_key_value_file' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,170 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,277 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'query_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,292 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,300 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_maker' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,308 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'table_compute' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,324 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,450 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,458 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,466 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,599 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'merge_cols' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,605 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'merge_cols' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,612 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,622 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_viterbi' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,629 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_indelqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,635 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,645 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_alnqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,652 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,675 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift_genesets' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,681 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift_dbnsfp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,688 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,722 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,766 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpfreqplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,773 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sniffles' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,780 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jasminesv' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,787 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpfreqplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,793 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,802 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,814 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,833 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,850 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,880 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,898 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'diff' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,903 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'unicycler' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,910 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'spades' from owner 'nml' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,917 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'miniasm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,923 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'racon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,929 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,948 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pharmcat' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,955 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name '10x_bamtofastq' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,962 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,970 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,977 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,986 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'chromeister' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:04,993 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,004 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'modify_loom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,009 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,017 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-08-30 12:46:05,023 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0': a when tag has not been defined for 'add_metadata (add_metadata_file) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,025 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils_empty_drops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,030 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspectclusters' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,041 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_filtnormconf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,050 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,060 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_trajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,067 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspecttrajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,076 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'alevin' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,086 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmonquantmerge' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,093 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'slice_image' from owner 'imgteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,097 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_create_qcmetric_ready_sce' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,103 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_tsne' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,109 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,116 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,120 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_dist_scatter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,126 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_exprs_freq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,133 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_pca' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,139 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_cluster_reduce_dimension' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,150 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,158 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,171 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,177 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-08-30 12:46:05,225 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1': a when tag has been defined for 'method (method) --> pl.rank_genes_groups_violin', but does not appear to be selectable. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,245 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_remove_confounders' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,253 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_parameter_iterator' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,259 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'droplet_barcode_plot' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,264 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,271 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gtf2gene_list' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,278 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon_kallisto_mtx_to_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,284 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sceasy_convert' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,293 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_ops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-08-30 12:46:05,298 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/0.0.3+galaxy0': a when tag has not been defined for 'copy_u (default) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,300 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'retrieve_scxa' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,306 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'music_inspect_eset' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-08-30 12:46:05,311 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'rdata.eset', which is used in the 'format' attribute of parameter 'rds_eset' +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,313 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'music_construct_eset' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,320 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspectclusters' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,330 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,338 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_trajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,344 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspecttrajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,355 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'alevin' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,364 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_create_qcmetric_ready_sce' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,370 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,377 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_dist_scatter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,382 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_pca' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,387 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-08-30 12:46:05,428 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0': a when tag has been defined for 'method (method) --> pl.rank_genes_groups_violin', but does not appear to be selectable. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,444 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,451 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon_kallisto_mtx_to_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,457 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_ops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-08-30 12:46:05,463 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.6.0+galaxy1': a when tag has not been defined for 'copy_u (default) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,466 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_cells' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,473 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_cells' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,481 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,488 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,495 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalise_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-08-30 12:46:05,501 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+3+galaxy0': a when tag has not been defined for 'exclude (exclude_highly_expressed) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,503 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalise_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-08-30 12:46:05,509 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.6.0+galaxy0': a when tag has not been defined for 'exclude (exclude_highly_expressed) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,511 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_variable_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,518 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_variable_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,525 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_scale_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,531 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_scale_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,539 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_pca' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,546 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_pca' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,553 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_compute_graph' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,559 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_compute_graph' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,567 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_tsne' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,574 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_tsne' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,581 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_umap' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,588 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_umap' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,597 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_cluster' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,604 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_cluster' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,612 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_markers' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,619 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_markers' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,627 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot_embed' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,633 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot_embed' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,641 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,648 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,657 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_filtnormconf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,666 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,735 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,743 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,749 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,757 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,765 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,786 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,793 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_groomer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,801 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_manipulation' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,810 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fasta_compute_length' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,816 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_paired_end_deinterlacer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,822 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_paired_end_interlacer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,828 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flash' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,836 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trim_galore' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,845 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,852 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,859 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,867 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,874 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,897 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,906 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,916 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'seq_filter_by_id' from owner 'peterjc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,924 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,948 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,963 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'length_and_gc_content' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,970 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'length_and_gc_content' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,978 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_reverse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,984 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,990 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_ops' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:05,999 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,006 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,013 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,211 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,452 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,678 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'map_param_value' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,685 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'compose_text_param' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,690 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gtftobed12' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,698 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_load' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,707 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_load' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,714 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_db_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,721 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_db_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,730 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,749 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,756 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__export' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,774 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__import' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,811 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mafft_add' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,819 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mafft' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,824 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mask' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,831 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__add_pseudocount' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,837 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__ancombc' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,845 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__tabulate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,852 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__ancom' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,859 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__trim_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,867 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__trim_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,875 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__demux_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,882 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__demux_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,892 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_pyro' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,897 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_ccs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,904 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,911 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,917 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__denoise_16s' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,923 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__denoise_other' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,930 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__visualize_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,936 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__emp_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,942 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__subsample_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,948 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__subsample_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,954 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,961 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__filter_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,968 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__emp_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,976 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_correlation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,985 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__adonis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:06,994 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__umap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,003 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__pcoa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,009 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__bioenv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,015 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__pcoa_biplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,022 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__tsne' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,028 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_group_significance' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,034 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__procrustes_analysis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,040 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__mantel' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,048 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,056 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_group_significance' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,062 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__core_metrics_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,070 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__core_metrics' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,080 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_correlation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,088 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__filter_distance_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,095 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,102 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,109 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,115 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_rarefaction' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,122 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_rarefaction' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,129 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__observed_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,135 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__bray_curtis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,141 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,149 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__alpha_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,155 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__shannon_entropy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,161 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__jaccard' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,167 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__pielou_evenness' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,173 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_phylogenetic_meta_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,181 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__weighted_unifrac' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,188 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__unweighted_unifrac' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,195 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_phylogenetic_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,201 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__faith_pd' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,209 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__procrustes_plot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,217 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__plot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,223 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__biplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,229 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,236 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__fit_classifier_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,243 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__fit_classifier_naive_bayes' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,251 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_consensus_blast' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,259 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__extract_reads' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,266 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_hybrid_vsearch_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,275 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_consensus_vsearch' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,284 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__blast' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,291 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__find_consensus_annotation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,297 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__vsearch_global' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,305 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__tabulate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,311 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__presence_absence' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,316 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,324 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,331 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_features_conditionally' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,337 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__rename_ids' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,344 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,350 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__relative_frequency' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,355 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,362 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,369 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__rarefy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,374 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__transpose' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,381 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__subsample' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,387 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,396 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge_taxa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,403 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__core_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,407 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__group' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,414 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,420 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__sepp' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,428 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__classify_otus_experimental' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,433 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__filter_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,439 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,446 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__correlation_clustering' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,451 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__dendrogram_heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,458 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__gradient_clustering' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,466 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic_ordination' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,474 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__assign_ids' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,480 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic_differential' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,487 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_hierarchical' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,492 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__pairwise_distances' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,500 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__feature_volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,509 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__nmit' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,514 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__first_differences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,520 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__plot_feature_volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,527 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__first_distances' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,533 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__linear_mixed_effects' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,542 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,549 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__pairwise_differences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,556 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__anova' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,562 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__maturity_index' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,571 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__shuffle_groups' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,577 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__distance_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,583 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__tabulate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,589 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__raxml_rapid_bootstrap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,916 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__fasttree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,923 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_iqtree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,932 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__iqtree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,941 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__robinson_foulds' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,947 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_raxml' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,953 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__filter_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,959 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__midpoint_root' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,964 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_fasttree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,972 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__raxml' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,978 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__filter_tree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,984 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__iqtree_ultrafast_bootstrap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:07,994 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_composition' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,003 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,009 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__filter_reads' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,015 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__bowtie2_build' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,022 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_taxonomy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,028 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__exclude_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,034 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_filter__q_score' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,042 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__metatable' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,048 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__fit_classifier' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,055 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__regress_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,061 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,069 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__scatterplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,076 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples_from_dist' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,084 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__confusion_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,092 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__split_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,099 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,104 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,113 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples_ncv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,119 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__fit_regressor' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,125 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__predict_classification' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,130 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__regress_samples_ncv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,136 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__predict_regression' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,143 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__collapse' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,149 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__filter_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,155 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__barplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,159 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__filter_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,165 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_closed_reference' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,170 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_open_reference' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,176 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__merge_pairs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,182 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__uchime_denovo' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,188 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__dereplicate_sequences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,194 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__fastq_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,200 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__uchime_ref' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,206 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_de_novo' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,214 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_build_pipeline' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,243 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_build_pipeline' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,272 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_searchcv' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,304 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_searchcv' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,324 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_parallel_coordinates_plot' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,330 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_parallel_coordinates_plot' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,336 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_ensemble' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,354 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_ensemble' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:08,373 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_regression_performance_plots' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-08-30 12:46:08,380 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:46:08,380 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:46:08,381 [pN:job_handler_0,p:8,tN:MainThread] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-08-30 12:46:08,381 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:46:08,381 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,381 [pN:job_handler_0,p:8,tN:MainThread] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,381 [pN:job_handler_0,p:8,tN:MainThread] Reading tools from config files finished (7763.663 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,382 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,406 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,412 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,421 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,421 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,423 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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,428 [pN:job_handler_0,p:8,tN:MainThread] Loading section: EMBOSS +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loading section: GATK +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loading section: NCBI BLAST+ +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357, version: 357 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loading section: GEMINI +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1, version: 0.20.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loading section: QIIME2 +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__export/qiime2_core__tools__export/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft_add/qiime2__alignment__mafft_add/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mask/qiime2__alignment__mask/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__add_pseudocount/qiime2__composition__add_pseudocount/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancombc/qiime2__composition__ancombc/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__tabulate/qiime2__composition__tabulate/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancom/qiime2__composition__ancom/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_single/qiime2__cutadapt__trim_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_paired/qiime2__cutadapt__trim_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_single/qiime2__cutadapt__demux_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_paired/qiime2__cutadapt__demux_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_pyro/qiime2__dada2__denoise_pyro/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_ccs/qiime2__dada2__denoise_ccs/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__deblur__denoise_16s/qiime2__deblur__denoise_16S/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__deblur__denoise_other/qiime2__deblur__denoise_other/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__deblur__visualize_stats/qiime2__deblur__visualize_stats/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__subsample_paired/qiime2__demux__subsample_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__subsample_single/qiime2__demux__subsample_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__pcoa_biplot/qiime2__diversity__pcoa_biplot/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__tsne/qiime2__diversity__tsne/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,447 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,447 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,447 [pN:job_handler_0,p:8,tN:MainThread] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,447 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,447 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,447 [pN:job_handler_0,p:8,tN:MainThread] Loading tool panel finished (65.070 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,452 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,452 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,452 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,452 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,452 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,452 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,452 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,452 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,453 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,453 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,453 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,453 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,453 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,453 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,453 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,453 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,453 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,454 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,460 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,460 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,460 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,460 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,460 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,460 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,461 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,461 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,462 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,463 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,464 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,465 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,466 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,467 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,468 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,468 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,468 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,468 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,469 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,470 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,472 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,473 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,474 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,475 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,476 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,477 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,478 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,481 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,482 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,483 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,483 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,483 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,483 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,483 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,483 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,483 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,483 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,483 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,484 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,485 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,495 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357, version: 357 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1, version: 0.20.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__export/qiime2_core__tools__export/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft_add/qiime2__alignment__mafft_add/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mask/qiime2__alignment__mask/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__extract_reads/qiime2__feature_classifier__extract_reads/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_consensus_vsearch/qiime2__feature_classifier__classify_consensus_vsearch/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__presence_absence/qiime2__feature_table__presence_absence/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__filter_samples/qiime2__feature_table__filter_samples/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,522 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-08-30 12:46:08,522 [pN:job_handler_0,p:8,tN:MainThread] Loading EDAM tool panel finished (74.728 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,581 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,581 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357, version: 357 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,581 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1, version: 0.20.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__export/qiime2_core__tools__export/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft_add/qiime2__alignment__mafft_add/2022.11.1+q2galaxy.2022.11.1.2, version: 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12:46:08,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancombc/qiime2__composition__ancombc/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__tabulate/qiime2__composition__tabulate/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancom/qiime2__composition__ancom/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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DEBUG 2024-08-30 12:46:08,584 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,584 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,584 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,585 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_de_novo/qiime2__vsearch__cluster_features_de_novo/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,595 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,596 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1, version: 1.0.8.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,596 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,596 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,596 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,596 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,596 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,596 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,598 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,598 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,598 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,598 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,598 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,598 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,598 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,598 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,598 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,598 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,599 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,599 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,599 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,599 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,599 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,599 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,599 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,599 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,599 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,600 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:08,600 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-08-30 12:46:08,600 [pN:job_handler_0,p:8,tN:MainThread] Loading EDAM tool panel finished (77.450 ms) +galaxy.tool_util.toolbox.integrated_panel DEBUG 2024-08-30 12:46:08,600 [pN:job_handler_0,p:8,tN:MainThread] Writing integrated tool panel config file to '/galaxy/server/config/mutable/integrated_tool_panel.xml' +galaxy.tool_util.deps.installable WARNING 2024-08-30 12:46:08,619 [pN:job_handler_0,p:8,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.installable WARNING 2024-08-30 12:46:08,623 [pN:job_handler_0,p:8,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.containers DEBUG 2024-08-30 12:46:08,625 [pN:job_handler_0,p:8,tN:MainThread] Loading container resolution config from file '/galaxy/server/config/container_resolvers_conf.xml' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'avivator' for datatype 'ome.tiff', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'q2view' for datatype 'qza', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'q2view' for datatype 'qzv', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,676 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,677 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,678 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,678 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,678 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,679 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,680 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,680 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,680 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,681 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,690 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,699 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,704 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,705 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,713 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,715 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,716 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,717 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,718 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,719 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,720 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,721 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,722 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,723 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,723 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,724 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,725 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,727 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,729 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,731 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,732 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,733 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,734 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,735 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,736 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,736 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,737 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,738 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,739 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,741 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,743 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,744 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,746 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,747 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,748 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,749 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,750 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,751 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,753 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,754 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,755 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,756 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,757 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,758 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,759 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,761 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,762 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,763 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,764 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,765 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,766 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,767 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,768 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,773 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,774 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,818 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,819 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,821 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,824 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,829 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,841 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,842 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:08,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:46:08,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:46:08,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:46:08,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:46:08,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded data fetch tool: __DATA_FETCH__ +sqlitedict DEBUG 2024-08-30 12:46:08,863 [pN:job_handler_0,p:8,tN:MainThread] closing SqliteDict(/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite) +sqlitedict.SqliteMultithread DEBUG 2024-08-30 12:46:08,864 [pN:job_handler_0,p:8,tN:Thread-2] received: --close--, send: --no more-- +sqlitedict DEBUG 2024-08-30 12:46:08,865 [pN:job_handler_0,p:8,tN:MainThread] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite' +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,870 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: PCA_3Dplot +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,871 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,871 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,872 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,872 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,873 [pN:job_handler_0,p:8,tN:MainThread] Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,874 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,874 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,875 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,876 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,878 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: editor +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,879 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,879 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,880 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: fits_image_viewer +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,881 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,882 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,883 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: h5web +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,886 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,889 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,890 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,890 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,891 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,892 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,894 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,897 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,900 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,902 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,905 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,905 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,906 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,906 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,907 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,908 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,909 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,909 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,910 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,911 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,913 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,915 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,917 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,919 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,921 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,923 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,924 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,926 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,927 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,929 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,931 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,933 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,935 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,936 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,936 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,937 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,938 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,939 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,940 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,940 [pN:job_handler_0,p:8,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping... +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,941 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,943 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: ts_visjs +galaxy.visualization.plugins.config_parser INFO 2024-08-30 12:46:08,943 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,944 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2024-08-30 12:46:08,945 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.tours._impl INFO 2024-08-30 12:46:08,965 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.history' +galaxy.tours._impl INFO 2024-08-30 12:46:08,973 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.windows' +galaxy.tours._impl INFO 2024-08-30 12:46:08,989 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.deferred' +galaxy.tours._impl INFO 2024-08-30 12:46:09,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.jobs.manager DEBUG 2024-08-30 12:46:09,011 [pN:job_handler_0,p:8,tN:MainThread] Initializing job handler +galaxy.jobs INFO 2024-08-30 12:46:09,011 [pN:job_handler_0,p:8,tN:MainThread] Handler 'job_handler_0' will load all configured runner plugins +galaxy.jobs.runners DEBUG 2024-08-30 12:46:09,013 [pN:job_handler_0,p:8,tN:MainThread] Loading KubernetesRunner with params: {'k8s_cleanup_job': 'onsuccess', 'k8s_fs_group_id': '101', 'k8s_galaxy_instance_id': 'prod-24-08-30-12-32-1-galaxy', 'k8s_interactivetools_ingress_annotations': '\nnginx.ingress.kubernetes.io/auth-tls-pass-certificate-to-upstream: "true"\nnginx.ingress.kubernetes.io/auth-tls-secret: \'prod-24-08-30-12-32-1/ca-secret\'\nnginx.ingress.kubernetes.io/auth-tls-verify-client: "on"\nnginx.ingress.kubernetes.io/auth-tls-verify-depth: "1"\nnginx.ingress.kubernetes.io/proxy-body-size: 10G\nnginx.ingress.kubernetes.io/proxy-read-timeout: "600"\nnginx.ingress.kubernetes.io/ssl-redirect: "true"\n', 'k8s_interactivetools_use_ssl': True, 'k8s_job_ttl_secs_after_finished': 90, 'k8s_namespace': 'prod-24-08-30-12-32-1', 'k8s_node_selector': 'cloud.google.com/gke-nodepool: default-pool', 'k8s_persistent_volume_claims': 'prod-24-08-30-12-32-1-galaxy-galaxy-pvc:/galaxy/server/database,prod-24-08-30-12-32-1-galaxy-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org,prod-24-08-30-12-32-1-galaxy-galaxy-pvc/cvmfsclone:/cvmfs/cloud.galaxyproject.org', 'k8s_pod_priority_class': 'prod-24-08-30-12-32-1-priority-class', 'k8s_pull_policy': 'IfNotPresent', 'k8s_supplemental_group_id': '101', 'k8s_use_service_account': True} +galaxy.jobs.runners.state_handler_factory DEBUG 2024-08-30 12:46:09,014 [pN:job_handler_0,p:8,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners.util.pykube_util ERROR 2024-08-30 12:46:09,014 [pN:job_handler_0,p:8,tN:MainThread] Galaxy instance [prod-24-08-30-12-32-1-galaxy] is either too long (>20 characters) or it includes non DNS acceptable characters, ignoring it. +galaxy.jobs DEBUG 2024-08-30 12:46:09,015 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.kubernetes:KubernetesJobRunner' as 'k8s' +galaxy.jobs.runners.state_handler_factory DEBUG 2024-08-30 12:46:09,015 [pN:job_handler_0,p:8,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs DEBUG 2024-08-30 12:46:09,015 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.handler DEBUG 2024-08-30 12:46:09,016 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runners plugins: k8s:local +galaxy.jobs.runners DEBUG 2024-08-30 12:46:09,022 [pN:job_handler_0,p:8,tN:MainThread] Starting 4 KubernetesRunner workers +galaxy.jobs.runners DEBUG 2024-08-30 12:46:09,025 [pN:job_handler_0,p:8,tN:MainThread] Starting 4 LocalRunner workers +galaxy.jobs.handler DEBUG 2024-08-30 12:46:09,028 [pN:job_handler_0,p:8,tN:MainThread] Handler queue starting for jobs assigned to handler: job_handler_0 +galaxy.jobs.handler INFO 2024-08-30 12:46:09,042 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'db-skip-locked' assignment method for handler 'job_handler_0', tag(s): _default_ +galaxy.jobs.handler INFO 2024-08-30 12:46:09,044 [pN:job_handler_0,p:8,tN:MainThread] job handler queue started +galaxy.jobs.handler INFO 2024-08-30 12:46:09,045 [pN:job_handler_0,p:8,tN:MainThread] job handler stop queue started +galaxy.web_stack.handlers DEBUG 2024-08-30 12:46:09,066 [pN:job_handler_0,p:8,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2024-08-30 12:46:09,066 [pN:job_handler_0,p:8,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2024-08-30 12:46:09,066 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.web_stack.handlers INFO 2024-08-30 12:46:09,097 [pN:job_handler_0,p:8,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on to override the default +galaxy.workflow.scheduling_manager INFO 2024-08-30 12:46:09,097 [pN:job_handler_0,p:8,tN:MainThread] Workflow scheduling handler assignment method(s): db-skip-locked +galaxy.workflow.scheduling_manager INFO 2024-08-30 12:46:09,097 [pN:job_handler_0,p:8,tN:MainThread] Tag [schedulers] handlers: workflow_scheduler0 +galaxy.web_stack.handlers DEBUG 2024-08-30 12:46:09,097 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.queue_worker INFO 2024-08-30 12:46:09,112 [pN:job_handler_0,p:8,tN:MainThread] Binding and starting galaxy control worker for job_handler_0 +galaxy.queue_worker INFO 2024-08-30 12:46:09,115 [pN:job_handler_0,p:8,tN:MainThread] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.model.database_heartbeat DEBUG 2024-08-30 12:46:09,126 [pN:job_handler_0,p:8,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is config watcher +galaxy.app INFO 2024-08-30 12:46:09,159 [pN:job_handler_0,p:8,tN:MainThread] Galaxy app startup finished (15251.810 ms) +galaxy.web_stack INFO 2024-08-30 12:46:09,159 [pN:job_handler_0,p:8,tN:MainThread] Galaxy server instance 'job_handler_0' is running +galaxy.queue_worker INFO 2024-08-30 12:46:09,170 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-08-30 12:46:09,171 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +sqlitedict DEBUG 2024-08-30 12:46:23,341 [pN:job_handler_0,p:8,tN:Thread-4 (check)] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/tmp7rrnqxv3cache.sqlite.tmp' +sqlitedict.SqliteMultithread DEBUG 2024-08-30 12:46:23,349 [pN:job_handler_0,p:8,tN:Thread-3] received: --close--, send: --no more-- +sqlitedict DEBUG 2024-08-30 12:46:23,372 [pN:job_handler_0,p:8,tN:Thread-4 (check)] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/tmp7rrnqxv3cache.sqlite.tmp' +galaxy.tools.cache DEBUG 2024-08-30 12:46:23,374 [pN:job_handler_0,p:8,tN:Thread-4 (check)] Exception while checking tools to remove from cache: file /cvmfs/cloud.galaxyproject.org/var/tool_cache/tmp7rrnqxv3cache.sqlite.tmp does not exist +galaxy.tools.cache DEBUG 2024-08-30 12:46:23,374 [pN:job_handler_0,p:8,tN:Thread-4 (check)] Removed the following tools from cache: ['toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2', 'toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering', 'raceid_clustering'] +galaxy.queue_worker INFO 2024-08-30 12:46:23,374 [pN:job_handler_0,p:8,tN:Thread-4 (check)] Queuing sync task reload_toolbox for job_handler_0. +galaxy.queue_worker INFO 2024-08-30 12:46:23,377 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2024-08-30 12:46:23,377 [pN:job_handler_0,p:8,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +sqlitedict.SqliteMultithread DEBUG 2024-08-30 12:46:23,378 [pN:job_handler_0,p:8,tN:Thread-7] received: --close--, send: --no more-- +galaxy.util WARNING 2024-08-30 12:46:23,426 [pN:job_handler_0,p:8,tN:Thread-1] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2024-08-30 12:46:23,433 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:46:23,433 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,434 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:46:23,434 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:46:23,435 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:46:23,437 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:46:23,437 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:46:23,439 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 865, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1092, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 530, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 546, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 802, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 799, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1123, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1414, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1622, in parse_param_elem + param = ToolParameter.build(self, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 319, in build + return parameter_types[param_type](tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2044, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1832, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 178, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 50, in from_element + return validator_types[_type].from_element(param, elem) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 727, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-08-30 12:46:23,440 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:46:23,440 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,451 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:46:23,513 [pN:job_handler_0,p:8,tN:Thread-1] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +sqlitedict DEBUG 2024-08-30 12:46:23,514 [pN:job_handler_0,p:8,tN:Thread-1] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite' +sqlitedict DEBUG 2024-08-30 12:46:23,567 [pN:job_handler_0,p:8,tN:Thread-1] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/tmp4pswy5mxcache.sqlite.tmp' +sqlitedict.SqliteMultithread DEBUG 2024-08-30 12:46:23,576 [pN:job_handler_0,p:8,tN:Thread-8] received: --close--, send: --no more-- +galaxy.tools WARNING 2024-08-30 12:46:23,600 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:46:23,600 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:46:23,600 [pN:job_handler_0,p:8,tN:Thread-1] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-08-30 12:46:23,600 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:46:23,600 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,600 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,600 [pN:job_handler_0,p:8,tN:Thread-1] Reading tools from config files finished (167.331 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,600 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,605 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,611 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,613 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,615 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,616 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,620 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,632 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,633 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,634 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,635 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,636 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,637 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,637 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,637 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,637 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,637 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,637 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,637 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,637 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,637 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,637 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,638 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,639 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,640 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,640 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,640 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,640 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,640 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,640 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,640 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,640 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,640 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,640 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,641 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,642 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,642 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,642 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,642 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,642 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,642 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,642 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,642 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,642 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,643 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,643 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,643 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,651 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1, version: 3.3.2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,651 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,651 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,651 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0, version: 3.3.2.0.0 into tool 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version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,651 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,652 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: GATK +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,652 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: NCBI BLAST+ +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,652 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357, version: 357 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,652 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: GEMINI +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1, version: 0.20.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,653 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: QIIME2 +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__export/qiime2_core__tools__export/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,670 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,671 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,671 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,671 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,671 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,671 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,671 [pN:job_handler_0,p:8,tN:Thread-1] Loading tool panel finished (70.308 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,675 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,676 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,676 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,676 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,676 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,676 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,676 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,676 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,676 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,677 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,678 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,679 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,680 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,681 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,681 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,681 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,681 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,681 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,681 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,681 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,681 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,681 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,682 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,683 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,684 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,685 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,686 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,687 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,688 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,689 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,690 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,691 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,692 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,693 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,694 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,695 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,696 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,697 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,698 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,699 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,700 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,701 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,702 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,703 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,704 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,705 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,706 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,707 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,708 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,709 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,710 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,711 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,711 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,711 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,712 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,713 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,713 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,713 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,713 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2024-08-30 12:46:23,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.6.0+galaxy1, version: 1.6.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+3+galaxy0, version: 1.8.1+3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,719 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,719 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DEBUG 2024-08-30 12:46:23,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,730 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 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DEBUG 2024-08-30 12:46:23,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,738 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,739 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,740 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,740 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,741 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-08-30 12:46:23,741 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (69.674 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,745 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,746 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,747 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,748 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,749 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,750 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,751 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,752 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,753 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,754 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,755 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,756 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,757 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,758 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,759 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,760 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,761 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,762 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,763 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,764 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,764 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,764 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,764 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,764 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,764 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,765 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,766 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,767 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,768 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,769 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,770 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,771 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,772 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,773 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,774 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,775 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,776 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,777 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,778 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,790 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,790 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,790 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,796 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,796 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,827 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:46:23,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-08-30 12:46:23,827 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (86.137 ms) +galaxy.tool_util.toolbox.integrated_panel DEBUG 2024-08-30 12:46:23,827 [pN:job_handler_0,p:8,tN:Thread-1] Writing integrated tool panel config file to '/galaxy/server/config/mutable/integrated_tool_panel.xml' +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-08-30 12:46:23,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:46:23,866 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:46:23,867 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:46:23,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:46:23,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +sqlitedict DEBUG 2024-08-30 12:46:23,886 [pN:job_handler_0,p:8,tN:Thread-1] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/tmp4pswy5mxcache.sqlite.tmp' +galaxy.queue_worker ERROR 2024-08-30 12:46:23,888 [pN:job_handler_0,p:8,tN:Thread-1] Error running control task type: reload_toolbox +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/queue_worker.py", line 393, in process_task + result = f(self.app, **body["kwargs"]) + File "/galaxy/server/lib/galaxy/queue_worker.py", line 166, in reload_toolbox + _get_new_toolbox(app, save_integrated_tool_panel) + File "/galaxy/server/lib/galaxy/queue_worker.py", line 188, in _get_new_toolbox + app.toolbox.persist_cache() + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 475, in persist_cache + region.persist() + File "/galaxy/server/lib/galaxy/tools/cache.py", line 98, in persist + self.reopen_ro() + File "/galaxy/server/lib/galaxy/tools/cache.py", line 66, in reopen_ro + self._get_cache(flag="r") + File "/galaxy/server/lib/galaxy/tools/cache.py", line 55, in _get_cache + self._cache = SqliteDict(cache_file, flag=flag, encode=encoder, decode=decoder, autocommit=False) + File "/galaxy/server/.venv/lib/python3.10/site-packages/sqlitedict.py", line 224, in __init__ + if self.tablename not in SqliteDict.get_tablenames(self.filename): + File "/galaxy/server/.venv/lib/python3.10/site-packages/sqlitedict.py", line 362, in get_tablenames + raise IOError('file %s does not exist' % (filename)) +OSError: file /cvmfs/cloud.galaxyproject.org/var/tool_cache/tmp4pswy5mxcache.sqlite.tmp does not exist +sqlitedict.SqliteMultithread DEBUG 2024-08-30 12:46:23,892 [pN:job_handler_0,p:8,tN:Thread-10] received: --close--, send: --no more-- +galaxy.queue_worker INFO 2024-08-30 12:46:23,904 [pN:job_handler_0,p:8,tN:Thread-4 (check)] Sending reload_toolbox control task. +galaxy.model.database_heartbeat DEBUG 2024-08-30 12:47:09,141 [pN:job_handler_0,p:8,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is not config watcher +galaxy.queue_worker INFO 2024-08-30 12:47:25,156 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2024-08-30 12:47:25,156 [pN:job_handler_0,p:8,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2024-08-30 12:47:25,181 [pN:job_handler_0,p:8,tN:Thread-1] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2024-08-30 12:47:25,186 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:47:25,187 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,187 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:47:25,189 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:47:25,189 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:47:25,191 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:47:25,191 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-08-30 12:47:25,193 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 865, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1092, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 530, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 546, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 802, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 799, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1123, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1414, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1622, in parse_param_elem + param = ToolParameter.build(self, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 319, in build + return parameter_types[param_type](tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2044, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1832, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 178, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 50, in from_element + return validator_types[_type].from_element(param, elem) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 727, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-08-30 12:47:25,195 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:47:25,195 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tool_util.toolbox.base WARNING 2024-08-30 12:47:25,235 [pN:job_handler_0,p:8,tN:Thread-1] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +sqlitedict DEBUG 2024-08-30 12:47:25,235 [pN:job_handler_0,p:8,tN:Thread-1] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite' +galaxy.tools WARNING 2024-08-30 12:47:25,272 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:47:25,272 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:47:25,272 [pN:job_handler_0,p:8,tN:Thread-1] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-08-30 12:47:25,272 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-08-30 12:47:25,272 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,273 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,273 [pN:job_handler_0,p:8,tN:Thread-1] Reading tools from config files finished (87.204 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,273 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,273 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,273 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,273 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,273 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,274 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,275 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,276 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,277 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,278 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,279 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,280 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,281 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,282 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,282 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,282 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,282 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,282 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,282 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,282 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,282 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,283 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,284 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,284 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,284 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,284 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,284 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,284 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,284 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,284 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,284 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,284 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,285 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,286 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,286 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,286 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,286 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,286 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,286 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,286 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,286 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,286 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,286 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,287 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,288 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,289 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,290 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,290 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,290 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,290 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,290 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,290 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,290 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,290 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,290 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,290 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,291 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,296 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,297 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,298 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,298 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,298 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,298 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,298 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,298 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,298 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,298 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,298 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,299 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,300 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,301 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,302 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,305 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,308 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,308 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,308 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,308 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,308 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,308 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,308 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,308 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,308 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,309 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,309 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,309 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,309 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,309 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,309 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,309 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,309 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,309 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,311 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,312 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,313 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,313 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,313 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,313 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,313 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,313 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,313 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,313 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,313 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,314 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,314 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,314 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,314 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,314 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,315 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,315 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,315 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,315 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,315 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,315 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,318 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,318 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,337 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,339 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toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,341 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,341 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,341 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,341 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,341 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,341 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,341 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,341 [pN:job_handler_0,p:8,tN:Thread-1] Loading tool panel finished (68.027 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,359 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,359 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,359 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,360 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,360 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,360 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,360 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2024-08-30 12:47:25,403 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,403 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,403 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,409 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,409 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,409 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,410 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,410 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,410 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,410 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,410 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,410 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,411 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,411 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,411 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,411 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,411 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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12:47:25,413 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-08-30 12:47:25,413 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (72.051 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,417 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,417 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,418 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,418 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,418 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,418 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,418 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,418 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,419 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,419 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,419 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,419 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,419 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,419 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,421 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,421 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,421 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,421 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,421 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,421 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,421 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,421 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,421 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,422 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,422 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,422 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,422 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,422 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,422 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,422 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,422 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,423 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,423 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,423 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,423 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,423 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,423 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,423 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,423 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,424 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,424 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,424 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,424 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,424 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,424 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,424 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,425 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,425 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,425 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,425 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,425 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,425 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,425 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,427 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,428 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,429 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,429 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,429 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,429 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__dereplicate_sequences/qiime2__vsearch__dereplicate_sequences/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,483 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__fastq_stats/qiime2__vsearch__fastq_stats/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,483 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_ref/qiime2__vsearch__uchime_ref/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,483 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_de_novo/qiime2__vsearch__cluster_features_de_novo/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,483 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,483 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1, version: 1.0.8.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,483 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,483 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,483 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,483 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,484 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,485 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (72.496 ms) +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,486 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,487 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,488 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,489 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,490 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,491 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,492 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,493 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,494 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,494 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,494 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,494 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,494 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,494 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-08-30 12:47:25,495 [pN:job_handler_0,p:8,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:47:25,496 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:47:25,497 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:47:25,498 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-08-30 12:47:25,499 [pN:job_handler_0,p:8,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2024-08-30 12:47:25,499 [pN:job_handler_0,p:8,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2024-08-30 12:47:25,500 [pN:job_handler_0,p:8,tN:Thread-1] Toolbox reload (343.832 ms) +galaxy.queue_worker INFO 2024-08-30 12:47:25,501 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-08-30 12:47:25,501 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.jobs.handler DEBUG 2024-08-30 12:48:44,849 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 1 +tpv.rules.gateway INFO 2024-08-30 12:48:44,894 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] loading tpv rules from: ['https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml', 'lib/galaxy/jobs/rules/tpv_rules_local.yml', 'https://gist.githubusercontent.com/afgane/68d1dbbe0af2468ba347dc74b6d3f7fa/raw/20edda50161bdcb74ff38935e7f76d79bfdaf303/tvp_rules_tests.yml'] +tpv.rules.gateway INFO 2024-08-30 12:48:45,394 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Watching for changes in file: lib/galaxy/jobs/rules/tpv_rules_local.yml +tpv.core.entities DEBUG 2024-08-30 12:48:45,497 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:48:45,498 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:48:45,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:48:45,544 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:48:45,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Working directory for job is: /galaxy/server/database/jobs_directory/000/1 +galaxy.jobs.runners DEBUG 2024-08-30 12:48:45,607 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [1] queued (93.533 ms) +galaxy.jobs.handler INFO 2024-08-30 12:48:45,613 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:48:45,622 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 1 +galaxy.jobs DEBUG 2024-08-30 12:48:45,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [1] prepared (152.237 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:48:45,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/1/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/1/registry.xml' '/galaxy/server/database/jobs_directory/000/1/upload_params.json' '1:/galaxy/server/database/objects/8/f/5/dataset_8f5e1da9-3cda-44a5-b232-ed8c7392632c_files:/galaxy/server/database/objects/8/f/5/dataset_8f5e1da9-3cda-44a5-b232-ed8c7392632c.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:48:45,846 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (1) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/1/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/1/galaxy_1.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:49:05,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 1: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:49:10,707 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 1 finished +galaxy.model.metadata DEBUG 2024-08-30 12:49:10,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 1 +galaxy.jobs INFO 2024-08-30 12:49:10,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 1 in /galaxy/server/database/jobs_directory/000/1 +galaxy.jobs DEBUG 2024-08-30 12:49:10,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 1 executed (165.934 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:49:12,216 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 2 +tpv.core.entities DEBUG 2024-08-30 12:49:12,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:49:12,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:49:12,261 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:49:12,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:49:12,300 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /galaxy/server/database/jobs_directory/000/2 +galaxy.jobs.runners DEBUG 2024-08-30 12:49:12,309 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [2] queued (48.328 ms) +galaxy.jobs.handler INFO 2024-08-30 12:49:12,313 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:49:12,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 2 +galaxy.jobs DEBUG 2024-08-30 12:49:12,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [2] prepared (79.936 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:49:12,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:49:12,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1: python:3.7 +galaxy.tool_util.deps.mulled.util DEBUG 2024-08-30 12:49:12,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Querying https://quay.io/api/v1/repository for repos within biocontainers +galaxy.tool_util.deps.containers INFO 2024-08-30 12:49:35,092 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:49:35,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/2/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/bce29ec10b78/sqlite_to_tabular/sqlite_to_tabular.py' --sqlitedb='/galaxy/server/database/objects/8/f/5/dataset_8f5e1da9-3cda-44a5-b232-ed8c7392632c.dat' --query_file='/galaxy/server/database/jobs_directory/000/2/configs/tmp1yved69q' --comment_char='#' --output='/galaxy/server/database/objects/2/3/5/dataset_23577869-cd1d-401b-b4ee-5aa263810431.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:49:35,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (2) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/2/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/2/galaxy_2.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:49:35,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:49:35,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:49:35,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:49:45,041 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 2: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:49:49,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 2 finished +galaxy.model.metadata DEBUG 2024-08-30 12:49:50,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 2 +galaxy.jobs INFO 2024-08-30 12:49:50,088 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 2 in /galaxy/server/database/jobs_directory/000/2 +galaxy.objectstore CRITICAL 2024-08-30 12:49:50,147 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmp1yved69q' +galaxy.jobs DEBUG 2024-08-30 12:49:50,147 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 2 executed (139.653 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:49:55,300 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 3 +tpv.core.entities DEBUG 2024-08-30 12:49:55,340 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:49:55,341 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:49:55,345 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:49:55,363 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:49:55,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Working directory for job is: /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs.runners DEBUG 2024-08-30 12:49:55,393 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [3] queued (47.848 ms) +galaxy.jobs.handler INFO 2024-08-30 12:49:55,396 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:49:55,401 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 3 +galaxy.jobs DEBUG 2024-08-30 12:49:55,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [3] prepared (102.649 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:49:55,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/3/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/3/registry.xml' '/galaxy/server/database/jobs_directory/000/3/upload_params.json' '3:/galaxy/server/database/objects/c/0/5/dataset_c0587c6b-3b82-4cf3-906f-37b653c8b64d_files:/galaxy/server/database/objects/c/0/5/dataset_c0587c6b-3b82-4cf3-906f-37b653c8b64d.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:49:55,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (3) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/3/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/3/galaxy_3.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:50:04,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 3: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:50:09,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 3 finished +galaxy.model.metadata DEBUG 2024-08-30 12:50:09,304 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 3 +galaxy.jobs INFO 2024-08-30 12:50:09,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 3 in /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs DEBUG 2024-08-30 12:50:09,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 3 executed (155.225 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:50:10,738 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 4 +tpv.core.entities DEBUG 2024-08-30 12:50:10,782 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*, abstract=False, cores=8, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:50:10,783 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:50:10,789 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:50:10,809 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:50:10,836 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Working directory for job is: /galaxy/server/database/jobs_directory/000/4 +galaxy.jobs.runners DEBUG 2024-08-30 12:50:10,846 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [4] queued (56.674 ms) +galaxy.jobs.handler INFO 2024-08-30 12:50:10,851 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:50:10,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 4 +galaxy.security.object_wrapper WARNING 2024-08-30 12:50:10,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to create dynamic subclass SafeStringWrapper__galaxy.model.none_like.None__NoneType__NotImplementedType__Number__SafeStringWrapper__ToolParameterValueWrapper__bool__bytearray__ellipsis for , None: type() doesn't support MRO entry resolution; use types.new_class() +galaxy.jobs DEBUG 2024-08-30 12:50:10,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [4] prepared (80.551 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:50:10,962 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:50:10,962 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:50:11,164 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:50:11,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/4/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/c/0/5/dataset_c0587c6b-3b82-4cf3-906f-37b653c8b64d.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a_files' && fastqc --outdir '/galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a_files' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a_files'/*\.html output.html] +galaxy.jobs.runners DEBUG 2024-08-30 12:50:11,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (4) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/4/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/4/galaxy_4.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/4/working/output.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/4/working/output.txt" "/galaxy/server/database/objects/8/d/2/dataset_8d259d6e-686d-4fac-baf0-ccde3d91bf7c.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/4/working/output.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/4/working/output.html" "/galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:50:11,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:50:11,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:50:11,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:50:28,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 4: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:50:33,711 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 4 finished +galaxy.model.metadata DEBUG 2024-08-30 12:50:33,772 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 5 +galaxy.model.metadata DEBUG 2024-08-30 12:50:33,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 4 +galaxy.util WARNING 2024-08-30 12:50:33,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/8/d/2/dataset_8d259d6e-686d-4fac-baf0-ccde3d91bf7c.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/8/d/2/dataset_8d259d6e-686d-4fac-baf0-ccde3d91bf7c.dat' +galaxy.util WARNING 2024-08-30 12:50:33,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a.dat' +galaxy.jobs INFO 2024-08-30 12:50:33,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 4 in /galaxy/server/database/jobs_directory/000/4 +galaxy.jobs DEBUG 2024-08-30 12:50:33,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 4 executed (163.578 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:50:38,476 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 5 +tpv.core.entities DEBUG 2024-08-30 12:50:38,512 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:50:38,513 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:50:38,518 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:50:38,535 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:50:38,558 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Working directory for job is: /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs.runners DEBUG 2024-08-30 12:50:38,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [5] queued (48.594 ms) +galaxy.jobs.handler INFO 2024-08-30 12:50:38,570 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:50:38,575 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 5 +galaxy.jobs DEBUG 2024-08-30 12:50:38,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [5] prepared (91.349 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:50:38,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/5/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/5/registry.xml' '/galaxy/server/database/jobs_directory/000/5/upload_params.json' '6:/galaxy/server/database/objects/0/9/3/dataset_093bc3f7-a38d-426a-891b-8a0bf1b6135c_files:/galaxy/server/database/objects/0/9/3/dataset_093bc3f7-a38d-426a-891b-8a0bf1b6135c.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:50:38,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (5) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/5/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/5/galaxy_5.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-08-30 12:50:39,575 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 6 +tpv.core.entities DEBUG 2024-08-30 12:50:39,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:50:39,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:50:39,621 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:50:39,638 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:50:39,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Working directory for job is: /galaxy/server/database/jobs_directory/000/6 +galaxy.jobs.runners DEBUG 2024-08-30 12:50:39,662 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [6] queued (41.118 ms) +galaxy.jobs.handler INFO 2024-08-30 12:50:39,665 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:50:39,671 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 6 +galaxy.jobs DEBUG 2024-08-30 12:50:39,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [6] prepared (100.486 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:50:39,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/6/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/6/registry.xml' '/galaxy/server/database/jobs_directory/000/6/upload_params.json' '7:/galaxy/server/database/objects/b/3/c/dataset_b3ccb58b-38b9-4a18-afbd-b672e05d2ab2_files:/galaxy/server/database/objects/b/3/c/dataset_b3ccb58b-38b9-4a18-afbd-b672e05d2ab2.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:50:39,830 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (6) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/6/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/6/galaxy_6.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:50:47,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 5: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:50:48,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 6: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:50:52,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 5 finished +galaxy.model.metadata DEBUG 2024-08-30 12:50:52,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 6 +galaxy.jobs INFO 2024-08-30 12:50:52,278 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 5 in /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs DEBUG 2024-08-30 12:50:52,335 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 5 executed (138.810 ms) +galaxy.jobs.runners DEBUG 2024-08-30 12:50:53,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 6 finished +galaxy.model.metadata DEBUG 2024-08-30 12:50:53,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 7 +galaxy.jobs INFO 2024-08-30 12:50:53,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 6 in /galaxy/server/database/jobs_directory/000/6 +galaxy.jobs DEBUG 2024-08-30 12:50:53,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 6 executed (135.115 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:50:53,996 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 7 +tpv.core.entities DEBUG 2024-08-30 12:50:54,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*, abstract=False, cores=8, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:50:54,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:50:54,050 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:50:54,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:50:54,098 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Working directory for job is: /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs.runners DEBUG 2024-08-30 12:50:54,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [7] queued (56.576 ms) +galaxy.jobs.handler INFO 2024-08-30 12:50:54,109 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:50:54,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 7 +galaxy.jobs DEBUG 2024-08-30 12:50:54,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [7] prepared (82.495 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:50:54,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:50:54,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:50:54,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:50:54,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/7/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/0/9/3/dataset_093bc3f7-a38d-426a-891b-8a0bf1b6135c.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e_files' && fastqc --outdir '/galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e_files' --contaminants '/galaxy/server/database/objects/b/3/c/dataset_b3ccb58b-38b9-4a18-afbd-b672e05d2ab2.dat' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e_files'/*\.html output.html] +galaxy.jobs.runners DEBUG 2024-08-30 12:50:54,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (7) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/7/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/7/galaxy_7.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/7/working/output.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/7/working/output.txt" "/galaxy/server/database/objects/e/6/c/dataset_e6cff499-28ac-43d0-bfa3-44f0a321f171.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/7/working/output.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/7/working/output.html" "/galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:50:54,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:50:54,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:50:54,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:51:01,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 7: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:51:06,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 7 finished +galaxy.model.metadata DEBUG 2024-08-30 12:51:06,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 9 +galaxy.model.metadata DEBUG 2024-08-30 12:51:06,647 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 8 +galaxy.util WARNING 2024-08-30 12:51:06,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/6/c/dataset_e6cff499-28ac-43d0-bfa3-44f0a321f171.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/6/c/dataset_e6cff499-28ac-43d0-bfa3-44f0a321f171.dat' +galaxy.util WARNING 2024-08-30 12:51:06,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e.dat' +galaxy.jobs INFO 2024-08-30 12:51:06,695 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 7 in /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs DEBUG 2024-08-30 12:51:06,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 7 executed (172.909 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:51:11,474 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 8 +tpv.core.entities DEBUG 2024-08-30 12:51:11,512 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:51:11,513 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:51:11,517 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:51:11,534 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:51:11,555 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Working directory for job is: /galaxy/server/database/jobs_directory/000/8 +galaxy.jobs.runners DEBUG 2024-08-30 12:51:11,563 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [8] queued (46.059 ms) +galaxy.jobs.handler INFO 2024-08-30 12:51:11,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:51:11,573 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 8 +galaxy.jobs DEBUG 2024-08-30 12:51:11,693 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [8] prepared (99.051 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:51:11,716 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/8/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/8/registry.xml' '/galaxy/server/database/jobs_directory/000/8/upload_params.json' '10:/galaxy/server/database/objects/6/3/7/dataset_637bb09e-fd66-434a-a23a-20571bc3766e_files:/galaxy/server/database/objects/6/3/7/dataset_637bb09e-fd66-434a-a23a-20571bc3766e.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:51:11,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (8) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/8/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/8/galaxy_8.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-08-30 12:51:12,570 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 9 +tpv.core.entities DEBUG 2024-08-30 12:51:12,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:51:12,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:51:12,614 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:51:12,631 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:51:12,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Working directory for job is: /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs.runners DEBUG 2024-08-30 12:51:12,658 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [9] queued (43.648 ms) +galaxy.jobs.handler INFO 2024-08-30 12:51:12,662 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:51:12,668 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 9 +galaxy.jobs DEBUG 2024-08-30 12:51:12,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [9] prepared (95.181 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:51:12,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/9/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/9/registry.xml' '/galaxy/server/database/jobs_directory/000/9/upload_params.json' '11:/galaxy/server/database/objects/2/5/5/dataset_25551fa7-9cbf-4974-b1e1-8caf0ab846b7_files:/galaxy/server/database/objects/2/5/5/dataset_25551fa7-9cbf-4974-b1e1-8caf0ab846b7.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:51:12,822 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (9) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/9/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/9/galaxy_9.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:51:20,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 8: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:51:21,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 9: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:51:26,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 8 finished +galaxy.model.metadata DEBUG 2024-08-30 12:51:26,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 10 +galaxy.jobs INFO 2024-08-30 12:51:26,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 8 in /galaxy/server/database/jobs_directory/000/8 +galaxy.jobs DEBUG 2024-08-30 12:51:26,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 8 executed (145.959 ms) +galaxy.jobs.runners DEBUG 2024-08-30 12:51:27,235 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 9 finished +galaxy.model.metadata DEBUG 2024-08-30 12:51:27,301 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 11 +galaxy.jobs INFO 2024-08-30 12:51:27,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 9 in /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs DEBUG 2024-08-30 12:51:27,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 9 executed (143.746 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:51:28,095 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 10 +tpv.core.entities DEBUG 2024-08-30 12:51:28,143 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*, abstract=False, cores=8, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:51:28,143 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:51:28,150 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:51:28,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:51:28,202 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Working directory for job is: /galaxy/server/database/jobs_directory/000/10 +galaxy.jobs.runners DEBUG 2024-08-30 12:51:28,212 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [10] queued (62.152 ms) +galaxy.jobs.handler INFO 2024-08-30 12:51:28,217 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:51:28,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 10 +galaxy.jobs DEBUG 2024-08-30 12:51:28,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [10] prepared (73.491 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:51:28,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:51:28,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:51:28,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:51:28,371 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/10/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/6/3/7/dataset_637bb09e-fd66-434a-a23a-20571bc3766e.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf_files' && fastqc --outdir '/galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf_files' --adapters '/galaxy/server/database/objects/2/5/5/dataset_25551fa7-9cbf-4974-b1e1-8caf0ab846b7.dat' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf_files'/*\.html output.html] +galaxy.jobs.runners DEBUG 2024-08-30 12:51:28,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (10) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/10/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/10/galaxy_10.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/10/working/output.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/10/working/output.txt" "/galaxy/server/database/objects/9/a/c/dataset_9ac06e3f-d38f-4f89-95c1-056016abfd3e.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/10/working/output.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/10/working/output.html" "/galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:51:28,413 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:51:28,413 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:51:28,433 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:51:36,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 10: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:51:41,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 10 finished +galaxy.model.metadata DEBUG 2024-08-30 12:51:41,172 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 13 +galaxy.model.metadata DEBUG 2024-08-30 12:51:41,201 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 12 +galaxy.util WARNING 2024-08-30 12:51:41,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/a/c/dataset_9ac06e3f-d38f-4f89-95c1-056016abfd3e.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/a/c/dataset_9ac06e3f-d38f-4f89-95c1-056016abfd3e.dat' +galaxy.util WARNING 2024-08-30 12:51:41,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf.dat' +galaxy.jobs INFO 2024-08-30 12:51:41,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 10 in /galaxy/server/database/jobs_directory/000/10 +galaxy.jobs DEBUG 2024-08-30 12:51:41,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 10 executed (194.863 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:51:46,643 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 11, 12 +tpv.core.entities DEBUG 2024-08-30 12:51:46,684 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:51:46,685 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:51:46,691 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:51:46,710 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:51:46,733 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Working directory for job is: /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs.runners DEBUG 2024-08-30 12:51:46,741 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [11] queued (50.532 ms) +galaxy.jobs.handler INFO 2024-08-30 12:51:46,745 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:51:46,751 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 11 +tpv.core.entities DEBUG 2024-08-30 12:51:46,766 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:51:46,767 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:51:46,775 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:51:46,793 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:51:46,824 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Working directory for job is: /galaxy/server/database/jobs_directory/000/12 +galaxy.jobs.runners DEBUG 2024-08-30 12:51:46,834 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [12] queued (58.377 ms) +galaxy.jobs.handler INFO 2024-08-30 12:51:46,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:51:46,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 12 +galaxy.jobs DEBUG 2024-08-30 12:51:46,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [11] prepared (121.307 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:51:46,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/11/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/11/registry.xml' '/galaxy/server/database/jobs_directory/000/11/upload_params.json' '14:/galaxy/server/database/objects/f/f/b/dataset_ffb6184f-a121-41b3-837c-8f3a099c9048_files:/galaxy/server/database/objects/f/f/b/dataset_ffb6184f-a121-41b3-837c-8f3a099c9048.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:51:46,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (11) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/11/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/11/galaxy_11.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-08-30 12:51:47,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [12] prepared (122.794 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:51:47,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/12/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/12/registry.xml' '/galaxy/server/database/jobs_directory/000/12/upload_params.json' '15:/galaxy/server/database/objects/c/e/b/dataset_ceb1cdac-974a-4475-a571-0208f86c0467_files:/galaxy/server/database/objects/c/e/b/dataset_ceb1cdac-974a-4475-a571-0208f86c0467.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:51:47,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (12) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/12/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/12/galaxy_12.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:51:55,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 12: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:51:55,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 11: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:52:00,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 12 finished +galaxy.jobs.runners DEBUG 2024-08-30 12:52:00,762 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 11 finished +galaxy.model.metadata DEBUG 2024-08-30 12:52:00,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 15 +galaxy.model.metadata DEBUG 2024-08-30 12:52:00,847 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 14 +galaxy.jobs INFO 2024-08-30 12:52:00,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 12 in /galaxy/server/database/jobs_directory/000/12 +galaxy.jobs INFO 2024-08-30 12:52:00,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 11 in /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs DEBUG 2024-08-30 12:52:00,933 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 12 executed (180.295 ms) +galaxy.jobs DEBUG 2024-08-30 12:52:00,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 11 executed (165.970 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:52:02,197 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 13 +tpv.core.entities DEBUG 2024-08-30 12:52:02,244 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*, abstract=False, cores=8, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:52:02,245 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:52:02,251 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:52:02,269 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:52:02,294 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Working directory for job is: /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs.runners DEBUG 2024-08-30 12:52:02,305 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [13] queued (53.450 ms) +galaxy.jobs.handler INFO 2024-08-30 12:52:02,309 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:52:02,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 13 +galaxy.jobs DEBUG 2024-08-30 12:52:02,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [13] prepared (81.990 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:52:02,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:52:02,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:52:02,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:52:02,473 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/13/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/f/f/b/dataset_ffb6184f-a121-41b3-837c-8f3a099c9048.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a_files' && fastqc --outdir '/galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a_files' --limits '/galaxy/server/database/objects/c/e/b/dataset_ceb1cdac-974a-4475-a571-0208f86c0467.dat' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a_files'/*\.html output.html] +galaxy.jobs.runners DEBUG 2024-08-30 12:52:02,502 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (13) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/13/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/13/galaxy_13.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/13/working/output.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/13/working/output.txt" "/galaxy/server/database/objects/9/8/3/dataset_983cc8d0-5f0b-4b1b-9496-40420a0f8288.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/13/working/output.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/13/working/output.html" "/galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:52:02,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:52:02,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:52:02,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:52:08,587 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 13: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:52:13,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 13 finished +galaxy.model.metadata DEBUG 2024-08-30 12:52:13,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 16 +galaxy.model.metadata DEBUG 2024-08-30 12:52:13,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 17 +galaxy.util WARNING 2024-08-30 12:52:13,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/8/3/dataset_983cc8d0-5f0b-4b1b-9496-40420a0f8288.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/8/3/dataset_983cc8d0-5f0b-4b1b-9496-40420a0f8288.dat' +galaxy.util WARNING 2024-08-30 12:52:13,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a.dat' +galaxy.jobs INFO 2024-08-30 12:52:13,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 13 in /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs DEBUG 2024-08-30 12:52:13,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 13 executed (176.336 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:52:18,680 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 14 +tpv.core.entities DEBUG 2024-08-30 12:52:18,716 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:52:18,717 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:52:18,723 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:52:18,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:52:18,766 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Working directory for job is: /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs.runners DEBUG 2024-08-30 12:52:18,774 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [14] queued (51.193 ms) +galaxy.jobs.handler INFO 2024-08-30 12:52:18,778 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:52:18,783 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 14 +galaxy.jobs DEBUG 2024-08-30 12:52:18,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [14] prepared (107.537 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:52:18,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/14/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/14/registry.xml' '/galaxy/server/database/jobs_directory/000/14/upload_params.json' '18:/galaxy/server/database/objects/1/d/9/dataset_1d93d954-96ce-4797-b8e8-11b2549144ec_files:/galaxy/server/database/objects/1/d/9/dataset_1d93d954-96ce-4797-b8e8-11b2549144ec.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:52:18,954 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (14) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/14/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/14/galaxy_14.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-08-30 12:52:19,780 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 15 +tpv.core.entities DEBUG 2024-08-30 12:52:19,819 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:52:19,820 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:52:19,825 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:52:19,845 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:52:19,866 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Working directory for job is: /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs.runners DEBUG 2024-08-30 12:52:19,874 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [15] queued (48.663 ms) +galaxy.jobs.handler INFO 2024-08-30 12:52:19,878 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:52:19,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 15 +galaxy.jobs DEBUG 2024-08-30 12:52:19,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [15] prepared (93.094 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:52:20,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/15/tool_script.sh] for tool command [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' '19:/galaxy/server/database/objects/3/5/d/dataset_35d5ef3b-89f7-4d65-add6-8b9bcf560943_files:/galaxy/server/database/objects/3/5/d/dataset_35d5ef3b-89f7-4d65-add6-8b9bcf560943.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:52:20,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (15) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/15/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/15/galaxy_15.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:52:27,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 14: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:52:29,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 15: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:52:33,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 14 finished +galaxy.model.metadata DEBUG 2024-08-30 12:52:33,101 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 18 +galaxy.jobs INFO 2024-08-30 12:52:33,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 14 in /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs DEBUG 2024-08-30 12:52:33,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 14 executed (139.593 ms) +galaxy.jobs.runners DEBUG 2024-08-30 12:52:34,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 15 finished +galaxy.model.metadata DEBUG 2024-08-30 12:52:34,292 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 19 +galaxy.jobs INFO 2024-08-30 12:52:34,336 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 15 in /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs DEBUG 2024-08-30 12:52:34,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 15 executed (149.368 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:52:35,286 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 16 +tpv.core.entities DEBUG 2024-08-30 12:52:35,330 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*, abstract=False, cores=8, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:52:35,331 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:52:35,337 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:52:35,354 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:52:35,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Working directory for job is: /galaxy/server/database/jobs_directory/000/16 +galaxy.jobs.runners DEBUG 2024-08-30 12:52:35,395 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [16] queued (57.983 ms) +galaxy.jobs.handler INFO 2024-08-30 12:52:35,399 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:52:35,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 16 +galaxy.jobs DEBUG 2024-08-30 12:52:35,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [16] prepared (77.226 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:52:35,505 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:52:35,505 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:52:35,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:52:35,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/16/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/1/d/9/dataset_1d93d954-96ce-4797-b8e8-11b2549144ec.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7_files' && fastqc --outdir '/galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7_files' --limits '/galaxy/server/database/objects/3/5/d/dataset_35d5ef3b-89f7-4d65-add6-8b9bcf560943.dat' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 3 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7_files'/*\.html output.html] +galaxy.jobs.runners DEBUG 2024-08-30 12:52:35,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (16) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/16/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/16/galaxy_16.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/16/working/output.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/16/working/output.html" "/galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/16/working/output.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/16/working/output.txt" "/galaxy/server/database/objects/c/4/0/dataset_c40250a1-d23d-4017-b352-0f1c9c7515d1.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:52:35,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:52:35,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:52:35,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:52:42,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 16: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:52:47,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 16 finished +galaxy.model.metadata DEBUG 2024-08-30 12:52:47,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 20 +galaxy.model.metadata DEBUG 2024-08-30 12:52:47,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 21 +galaxy.util WARNING 2024-08-30 12:52:47,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7.dat' +galaxy.util WARNING 2024-08-30 12:52:47,363 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/4/0/dataset_c40250a1-d23d-4017-b352-0f1c9c7515d1.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/4/0/dataset_c40250a1-d23d-4017-b352-0f1c9c7515d1.dat' +galaxy.jobs INFO 2024-08-30 12:52:47,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 16 in /galaxy/server/database/jobs_directory/000/16 +galaxy.jobs DEBUG 2024-08-30 12:52:47,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 16 executed (161.384 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:52:52,792 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 17 +tpv.core.entities DEBUG 2024-08-30 12:52:52,832 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:52:52,833 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:52:52,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:52:52,860 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:52:52,884 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Working directory for job is: /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs.runners DEBUG 2024-08-30 12:52:52,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [17] queued (51.818 ms) +galaxy.jobs.handler INFO 2024-08-30 12:52:52,895 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:52:52,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 17 +galaxy.jobs DEBUG 2024-08-30 12:52:53,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [17] prepared (96.624 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:52:53,043 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/17/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/17/registry.xml' '/galaxy/server/database/jobs_directory/000/17/upload_params.json' '22:/galaxy/server/database/objects/c/7/7/dataset_c779310f-6c04-4ec2-a7b8-ed0679e21e17_files:/galaxy/server/database/objects/c/7/7/dataset_c779310f-6c04-4ec2-a7b8-ed0679e21e17.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:52:53,057 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (17) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/17/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/17/galaxy_17.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:53:01,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 17: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:53:06,526 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 17 finished +galaxy.model.metadata DEBUG 2024-08-30 12:53:06,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 22 +galaxy.jobs INFO 2024-08-30 12:53:06,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 17 in /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs DEBUG 2024-08-30 12:53:06,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 17 executed (150.492 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:53:07,213 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 18 +tpv.core.entities DEBUG 2024-08-30 12:53:07,254 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*, abstract=False, cores=8, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:53:07,255 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:53:07,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:53:07,281 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:53:07,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Working directory for job is: /galaxy/server/database/jobs_directory/000/18 +galaxy.jobs.runners DEBUG 2024-08-30 12:53:07,317 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [18] queued (56.084 ms) +galaxy.jobs.handler INFO 2024-08-30 12:53:07,321 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:53:07,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 18 +galaxy.jobs DEBUG 2024-08-30 12:53:07,410 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [18] prepared (67.543 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:53:07,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:53:07,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:53:07,440 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:53:07,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/18/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/c/7/7/dataset_c779310f-6c04-4ec2-a7b8-ed0679e21e17.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files' && fastqc --outdir '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files' --threads ${GALAXY_SLOTS:-2} --quiet --extract --min_length 108 --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files'/*\.html output.html] +galaxy.jobs.runners DEBUG 2024-08-30 12:53:07,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (18) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/18/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/18/galaxy_18.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/18/working/output.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/18/working/output.html" "/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/18/working/output.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/18/working/output.txt" "/galaxy/server/database/objects/3/6/6/dataset_366f2433-d768-44fa-bae1-205e2035b74c.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:53:07,511 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:53:07,511 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:53:07,532 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2024-08-30 12:53:14,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.18.96.1:443/apis/batch/v1/namespaces/prod-24-08-30-12-32-1/jobs/gxy-lj7sk + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-lj7sk": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:53:14,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (18/gxy-lj7sk) Terminated at user's request +galaxy.util WARNING 2024-08-30 12:53:14,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264.dat' +galaxy.util WARNING 2024-08-30 12:53:14,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/6/6/dataset_366f2433-d768-44fa-bae1-205e2035b74c.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/6/6/dataset_366f2433-d768-44fa-bae1-205e2035b74c.dat' +galaxy.jobs.handler DEBUG 2024-08-30 12:53:18,564 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 19 +tpv.core.entities DEBUG 2024-08-30 12:53:18,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:53:18,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:53:18,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:53:18,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:53:18,659 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Working directory for job is: /galaxy/server/database/jobs_directory/000/19 +galaxy.jobs.runners DEBUG 2024-08-30 12:53:18,668 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [19] queued (51.727 ms) +galaxy.jobs.handler INFO 2024-08-30 12:53:18,672 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:53:18,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 19 +galaxy.jobs DEBUG 2024-08-30 12:53:18,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [19] prepared (94.607 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:53:18,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/19/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/19/registry.xml' '/galaxy/server/database/jobs_directory/000/19/upload_params.json' '25:/galaxy/server/database/objects/9/a/0/dataset_9a00d4ad-a9ba-44fc-8f09-8f4cb86209f3_files:/galaxy/server/database/objects/9/a/0/dataset_9a00d4ad-a9ba-44fc-8f09-8f4cb86209f3.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:53:18,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (19) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/19/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/19/galaxy_19.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:53:27,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 19: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:53:31,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 19 finished +galaxy.model.metadata DEBUG 2024-08-30 12:53:31,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 25 +galaxy.jobs INFO 2024-08-30 12:53:32,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 19 in /galaxy/server/database/jobs_directory/000/19 +galaxy.jobs DEBUG 2024-08-30 12:53:32,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 19 executed (132.416 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:53:32,982 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 20 +tpv.core.entities DEBUG 2024-08-30 12:53:33,018 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*, abstract=False, cores=8, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:53:33,019 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:53:33,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:53:33,041 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:53:33,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Working directory for job is: /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs.runners DEBUG 2024-08-30 12:53:33,074 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [20] queued (48.530 ms) +galaxy.jobs.handler INFO 2024-08-30 12:53:33,078 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:53:33,082 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 20 +galaxy.jobs DEBUG 2024-08-30 12:53:33,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [20] prepared (53.689 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:53:33,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:53:33,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:53:33,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:53:33,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/20/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/9/a/0/dataset_9a00d4ad-a9ba-44fc-8f09-8f4cb86209f3.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56_files' && fastqc --outdir '/galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56_files' --threads ${GALAXY_SLOTS:-2} --quiet --extract --nogroup --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56_files'/*\.html output.html] +galaxy.jobs.runners DEBUG 2024-08-30 12:53:33,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (20) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/20/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/20/galaxy_20.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/20/working/output.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/20/working/output.html" "/galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/20/working/output.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/20/working/output.txt" "/galaxy/server/database/objects/3/9/a/dataset_39a59496-43e8-4d2c-bf1e-4d87eea99427.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:53:33,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:53:33,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:53:33,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:53:41,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 20: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:53:46,425 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 20 finished +galaxy.model.metadata DEBUG 2024-08-30 12:53:46,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 26 +galaxy.model.metadata DEBUG 2024-08-30 12:53:46,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 27 +galaxy.util WARNING 2024-08-30 12:53:46,529 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56.dat' +galaxy.util WARNING 2024-08-30 12:53:46,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/9/a/dataset_39a59496-43e8-4d2c-bf1e-4d87eea99427.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/9/a/dataset_39a59496-43e8-4d2c-bf1e-4d87eea99427.dat' +galaxy.jobs INFO 2024-08-30 12:53:46,564 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 20 in /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs DEBUG 2024-08-30 12:53:46,630 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 20 executed (174.193 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:53:50,556 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 21 +tpv.core.entities DEBUG 2024-08-30 12:53:50,591 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:53:50,592 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:53:50,597 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:53:50,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:53:50,639 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Working directory for job is: /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs.runners DEBUG 2024-08-30 12:53:50,648 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [21] queued (50.315 ms) +galaxy.jobs.handler INFO 2024-08-30 12:53:50,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:53:50,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 21 +galaxy.jobs DEBUG 2024-08-30 12:53:50,781 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [21] prepared (103.235 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:53:50,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/21/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/21/registry.xml' '/galaxy/server/database/jobs_directory/000/21/upload_params.json' '28:/galaxy/server/database/objects/c/2/d/dataset_c2d9e4d7-8245-4adf-8f54-48436964c052_files:/galaxy/server/database/objects/c/2/d/dataset_c2d9e4d7-8245-4adf-8f54-48436964c052.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:53:50,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (21) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/21/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/21/galaxy_21.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:53:59,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 21: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:54:04,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 21 finished +galaxy.model.metadata DEBUG 2024-08-30 12:54:04,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 28 +galaxy.jobs INFO 2024-08-30 12:54:04,835 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 21 in /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs DEBUG 2024-08-30 12:54:04,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 21 executed (210.911 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:54:05,979 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 22 +tpv.core.entities DEBUG 2024-08-30 12:54:06,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*, abstract=False, cores=8, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:54:06,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:54:06,031 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:54:06,051 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:54:06,077 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Working directory for job is: /galaxy/server/database/jobs_directory/000/22 +galaxy.jobs.runners DEBUG 2024-08-30 12:54:06,087 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [22] queued (55.362 ms) +galaxy.jobs.handler INFO 2024-08-30 12:54:06,091 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:54:06,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 22 +galaxy.jobs DEBUG 2024-08-30 12:54:06,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [22] prepared (65.201 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:54:06,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:54:06,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:54:06,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:54:06,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/22/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/c/2/d/dataset_c2d9e4d7-8245-4adf-8f54-48436964c052.dat' 'hisat_output_1_bam' && mkdir -p '/galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b_files' && fastqc --outdir '/galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b_files' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 7 -f 'bam' 'hisat_output_1_bam' && cp '/galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b_files'/*\.html output.html] +galaxy.jobs.runners DEBUG 2024-08-30 12:54:06,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (22) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/22/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/22/galaxy_22.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/22/working/output.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/22/working/output.html" "/galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/22/working/output.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/22/working/output.txt" "/galaxy/server/database/objects/8/2/2/dataset_8223b98e-a5af-4f6b-be17-f355070397a5.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:54:06,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:54:06,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0: fastqc:0.11.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:54:06,292 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:54:13,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 22: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:54:18,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 22 finished +galaxy.model.metadata DEBUG 2024-08-30 12:54:18,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 29 +galaxy.model.metadata DEBUG 2024-08-30 12:54:18,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 30 +galaxy.util WARNING 2024-08-30 12:54:18,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b.dat' +galaxy.util WARNING 2024-08-30 12:54:18,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/8/2/2/dataset_8223b98e-a5af-4f6b-be17-f355070397a5.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/8/2/2/dataset_8223b98e-a5af-4f6b-be17-f355070397a5.dat' +galaxy.jobs INFO 2024-08-30 12:54:18,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 22 in /galaxy/server/database/jobs_directory/000/22 +galaxy.jobs DEBUG 2024-08-30 12:54:19,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 22 executed (181.376 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:54:24,516 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 23 +tpv.core.entities DEBUG 2024-08-30 12:54:24,552 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:54:24,553 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:54:24,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:54:24,580 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:54:24,602 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Working directory for job is: /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs.runners DEBUG 2024-08-30 12:54:24,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [23] queued (48.957 ms) +galaxy.jobs.handler INFO 2024-08-30 12:54:24,612 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:54:24,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 23 +galaxy.jobs DEBUG 2024-08-30 12:54:24,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [23] prepared (106.074 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:54:24,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/23/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/23/registry.xml' '/galaxy/server/database/jobs_directory/000/23/upload_params.json' '31:/galaxy/server/database/objects/c/7/7/dataset_c77f6a48-f5f4-4df1-b6bc-0a0bc393c562_files:/galaxy/server/database/objects/c/7/7/dataset_c77f6a48-f5f4-4df1-b6bc-0a0bc393c562.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:54:24,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (23) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/23/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/23/galaxy_23.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:54:32,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 23: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:54:38,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 23 finished +galaxy.model.metadata DEBUG 2024-08-30 12:54:38,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 31 +galaxy.jobs INFO 2024-08-30 12:54:38,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 23 in /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs DEBUG 2024-08-30 12:54:38,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 23 executed (147.880 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:54:38,961 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 24 +tpv.core.entities DEBUG 2024-08-30 12:54:39,002 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:54:39,003 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:54:39,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:54:39,028 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:54:39,052 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Working directory for job is: /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs.runners DEBUG 2024-08-30 12:54:39,061 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [24] queued (51.358 ms) +galaxy.jobs.handler INFO 2024-08-30 12:54:39,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:54:39,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 24 +galaxy.jobs DEBUG 2024-08-30 12:54:39,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [24] prepared (71.161 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:54:39,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:54:39,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:54:39,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:54:39,407 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/24/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/24/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T "${TMPDIR:-.}" -O sam -o coordsort.sam '/galaxy/server/database/objects/c/7/7/dataset_c77f6a48-f5f4-4df1-b6bc-0a0bc393c562.dat' && samtools markdup -@ $addthreads coordsort.sam '/galaxy/server/database/objects/4/6/c/dataset_46c868b5-8a19-4133-9b9e-3b7292714b5e.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:54:39,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (24) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/24/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/24/galaxy_24.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:54:39,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:54:39,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:54:39,460 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:54:46,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 24: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:54:51,142 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 24 finished +galaxy.model.metadata DEBUG 2024-08-30 12:54:51,210 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 32 +galaxy.jobs INFO 2024-08-30 12:54:51,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 24 in /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs DEBUG 2024-08-30 12:54:51,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 24 executed (181.525 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:54:53,415 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 25 +tpv.core.entities DEBUG 2024-08-30 12:54:53,462 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:54:53,462 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:54:53,469 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:54:53,487 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:54:53,507 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Working directory for job is: /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs.runners DEBUG 2024-08-30 12:54:53,515 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [25] queued (46.272 ms) +galaxy.jobs.handler INFO 2024-08-30 12:54:53,519 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:54:53,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 25 +galaxy.jobs DEBUG 2024-08-30 12:54:53,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [25] prepared (106.165 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:54:53,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/25/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/25/registry.xml' '/galaxy/server/database/jobs_directory/000/25/upload_params.json' '33:/galaxy/server/database/objects/9/8/8/dataset_988d51bd-daba-4ed9-a392-1ed7724aba4d_files:/galaxy/server/database/objects/9/8/8/dataset_988d51bd-daba-4ed9-a392-1ed7724aba4d.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:54:53,693 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (25) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/25/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/25/galaxy_25.ec; sh -c "exit $return_code" +sqlitedict.SqliteMultithread DEBUG 2024-08-30 12:55:02,786 [pN:job_handler_0,p:8,tN:Thread-6] received: --close--, send: --no more-- +sqlitedict.SqliteMultithread DEBUG 2024-08-30 12:55:02,817 [pN:job_handler_0,p:8,tN:Thread-9] received: --close--, send: --no more-- +galaxy.jobs.runners DEBUG 2024-08-30 12:55:03,025 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 25: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:55:08,163 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 25 finished +galaxy.model.metadata DEBUG 2024-08-30 12:55:08,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 33 +galaxy.jobs INFO 2024-08-30 12:55:08,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 25 in /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs DEBUG 2024-08-30 12:55:08,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 25 executed (145.865 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:55:08,968 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 26 +tpv.core.entities DEBUG 2024-08-30 12:55:09,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:55:09,010 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:55:09,016 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:55:09,035 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:55:09,058 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Working directory for job is: /galaxy/server/database/jobs_directory/000/26 +galaxy.jobs.runners DEBUG 2024-08-30 12:55:09,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [26] queued (51.217 ms) +galaxy.jobs.handler INFO 2024-08-30 12:55:09,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:55:09,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 26 +galaxy.jobs DEBUG 2024-08-30 12:55:09,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [26] prepared (56.823 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:09,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:55:09,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:09,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:55:09,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/26/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/26/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T "${TMPDIR:-.}" -O sam -o coordsort.sam '/galaxy/server/database/objects/9/8/8/dataset_988d51bd-daba-4ed9-a392-1ed7724aba4d.dat' && samtools markdup -@ $addthreads -r coordsort.sam '/galaxy/server/database/objects/a/6/6/dataset_a667be73-c02a-41a2-89f1-4bda7a51270c.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:55:09,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (26) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/26/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/26/galaxy_26.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:09,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:55:09,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:09,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2024-08-30 12:55:13,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.18.96.1:443/apis/batch/v1/namespaces/prod-24-08-30-12-32-1/jobs/gxy-f6mb4 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-f6mb4": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:55:13,083 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (26/gxy-f6mb4) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-08-30 12:55:15,195 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 27 +tpv.core.entities DEBUG 2024-08-30 12:55:15,232 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:55:15,233 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:55:15,240 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:55:15,259 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:55:15,283 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Working directory for job is: /galaxy/server/database/jobs_directory/000/27 +galaxy.jobs.runners DEBUG 2024-08-30 12:55:15,291 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [27] queued (50.836 ms) +galaxy.jobs.handler INFO 2024-08-30 12:55:15,295 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:55:15,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 27 +galaxy.jobs DEBUG 2024-08-30 12:55:15,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [27] prepared (107.419 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:55:15,451 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/27/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/27/registry.xml' '/galaxy/server/database/jobs_directory/000/27/upload_params.json' '35:/galaxy/server/database/objects/e/3/d/dataset_e3dd87f7-3c64-473c-8c3a-9c905ae7adc5_files:/galaxy/server/database/objects/e/3/d/dataset_e3dd87f7-3c64-473c-8c3a-9c905ae7adc5.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:55:15,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (27) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/27/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/27/galaxy_27.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:55:24,390 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 27: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:55:29,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 27 finished +galaxy.model.metadata DEBUG 2024-08-30 12:55:29,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 35 +galaxy.jobs INFO 2024-08-30 12:55:29,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 27 in /galaxy/server/database/jobs_directory/000/27 +galaxy.jobs DEBUG 2024-08-30 12:55:29,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 27 executed (196.858 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:55:30,647 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 28 +tpv.core.entities DEBUG 2024-08-30 12:55:30,688 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:55:30,689 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:55:30,694 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:55:30,714 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:55:30,734 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Working directory for job is: /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs.runners DEBUG 2024-08-30 12:55:30,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [28] queued (48.885 ms) +galaxy.jobs.handler INFO 2024-08-30 12:55:30,747 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:55:30,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 28 +galaxy.jobs DEBUG 2024-08-30 12:55:30,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [28] prepared (59.050 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:30,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:55:30,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:30,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:55:30,889 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/28/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/28/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/e/3/d/dataset_e3dd87f7-3c64-473c-8c3a-9c905ae7adc5.dat' coordsort.sam && samtools markdup -@ $addthreads -S coordsort.sam '/galaxy/server/database/objects/1/5/1/dataset_15131c50-2549-4208-92bb-1aba16423f02.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:55:30,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (28) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/28/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/28/galaxy_28.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:30,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:55:30,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:30,940 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:55:35,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 28: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:55:40,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 28 finished +galaxy.model.metadata DEBUG 2024-08-30 12:55:40,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 36 +galaxy.jobs INFO 2024-08-30 12:55:40,826 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 28 in /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs DEBUG 2024-08-30 12:55:40,890 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 28 executed (185.376 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:55:43,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 29 +tpv.core.entities DEBUG 2024-08-30 12:55:43,056 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:55:43,057 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:55:43,061 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:55:43,077 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:55:43,093 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Working directory for job is: /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs.runners DEBUG 2024-08-30 12:55:43,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [29] queued (39.390 ms) +galaxy.jobs.handler INFO 2024-08-30 12:55:43,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:55:43,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 29 +galaxy.jobs DEBUG 2024-08-30 12:55:43,240 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [29] prepared (109.038 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:55:43,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/29/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/29/registry.xml' '/galaxy/server/database/jobs_directory/000/29/upload_params.json' '37:/galaxy/server/database/objects/7/4/4/dataset_7449b6ab-4847-4f4a-8ddb-9a2571745d7e_files:/galaxy/server/database/objects/7/4/4/dataset_7449b6ab-4847-4f4a-8ddb-9a2571745d7e.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:55:43,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (29) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/29/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/29/galaxy_29.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:55:51,724 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 29: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:55:56,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 29 finished +galaxy.model.metadata DEBUG 2024-08-30 12:55:56,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 37 +galaxy.jobs INFO 2024-08-30 12:55:56,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 29 in /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs DEBUG 2024-08-30 12:55:56,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 29 executed (142.856 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:55:57,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 30 +tpv.core.entities DEBUG 2024-08-30 12:55:57,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:55:57,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:55:57,498 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:55:57,516 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:55:57,544 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Working directory for job is: /galaxy/server/database/jobs_directory/000/30 +galaxy.jobs.runners DEBUG 2024-08-30 12:55:57,555 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [30] queued (56.656 ms) +galaxy.jobs.handler INFO 2024-08-30 12:55:57,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:55:57,565 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 30 +galaxy.jobs DEBUG 2024-08-30 12:55:57,648 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [30] prepared (59.279 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:57,648 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:55:57,648 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:57,679 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:55:57,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/30/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/30/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T "${TMPDIR:-.}" -O sam -o coordsort.sam '/galaxy/server/database/objects/7/4/4/dataset_7449b6ab-4847-4f4a-8ddb-9a2571745d7e.dat' && samtools markdup -@ $addthreads -s coordsort.sam '/galaxy/server/database/objects/a/0/e/dataset_a0ebcb53-0ac7-46ae-aa45-b18cf80d2005.dat' 2> '/galaxy/server/database/objects/2/f/f/dataset_2ffa50c5-3185-42eb-9a0f-4c908879a988.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:55:57,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (30) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/30/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/30/galaxy_30.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:57,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:55:57,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:55:57,771 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:56:03,026 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 30: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:56:08,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 30 finished +galaxy.model.metadata DEBUG 2024-08-30 12:56:08,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 38 +galaxy.model.metadata DEBUG 2024-08-30 12:56:08,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 39 +galaxy.jobs INFO 2024-08-30 12:56:08,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 30 in /galaxy/server/database/jobs_directory/000/30 +galaxy.jobs DEBUG 2024-08-30 12:56:08,308 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 30 executed (226.167 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:56:12,927 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 31 +tpv.core.entities DEBUG 2024-08-30 12:56:12,966 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:56:12,967 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:56:12,973 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:56:12,996 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:56:13,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Working directory for job is: /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs.runners DEBUG 2024-08-30 12:56:13,033 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [31] queued (60.241 ms) +galaxy.jobs.handler INFO 2024-08-30 12:56:13,037 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:56:13,043 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 31 +galaxy.jobs DEBUG 2024-08-30 12:56:13,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [31] prepared (109.653 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:56:13,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/31/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/31/registry.xml' '/galaxy/server/database/jobs_directory/000/31/upload_params.json' '40:/galaxy/server/database/objects/f/a/5/dataset_fa5c2641-183c-415d-9a5b-764b9dec32d7_files:/galaxy/server/database/objects/f/a/5/dataset_fa5c2641-183c-415d-9a5b-764b9dec32d7.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:56:13,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (31) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/31/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/31/galaxy_31.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:56:21,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 31: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:56:26,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 31 finished +galaxy.model.metadata DEBUG 2024-08-30 12:56:26,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 40 +galaxy.jobs INFO 2024-08-30 12:56:26,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 31 in /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs DEBUG 2024-08-30 12:56:26,781 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 31 executed (147.669 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:56:27,498 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 32 +tpv.core.entities DEBUG 2024-08-30 12:56:27,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:56:27,543 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:56:27,550 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:56:27,571 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:56:27,605 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Working directory for job is: /galaxy/server/database/jobs_directory/000/32 +galaxy.jobs.runners DEBUG 2024-08-30 12:56:27,615 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [32] queued (65.429 ms) +galaxy.jobs.handler INFO 2024-08-30 12:56:27,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:56:27,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 32 +galaxy.jobs DEBUG 2024-08-30 12:56:27,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [32] prepared (117.060 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:56:27,764 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:56:27,764 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10: mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:56:27,954 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:56:27,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/32/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/32/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/a/5/dataset_fa5c2641-183c-415d-9a5b-764b9dec32d7.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp -p 0 --aberrant "1.0,1.0" --BAF-weight 1.0 --BAF-dev "0.04,0.04" --LRR-weight 0.2 --LRR-dev "0.2,0.2" --LRR-smooth-win 10 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/0/7/6/dataset_0769d0b8-f60d-4d5d-94da-f071cb821c26.dat' && mv cnv_tmp/summary.*.tab '/galaxy/server/database/objects/d/8/a/dataset_d8aa9ded-1390-495a-9a76-aa639af0d205.dat' && (echo 'Copy-number variation plots (bcftools cnv)' > /galaxy/server/database/objects/a/2/a/dataset_a2a2705e-2b98-4a45-855f-12a54f0a9486.dat; for plot in cnv_tmp/*.png; do [ -f "$plot" ] || break; echo '
' >> /galaxy/server/database/objects/a/2/a/dataset_a2a2705e-2b98-4a45-855f-12a54f0a9486.dat; done; echo '' >> /galaxy/server/database/objects/a/2/a/dataset_a2a2705e-2b98-4a45-855f-12a54f0a9486.dat;)] +galaxy.jobs.runners DEBUG 2024-08-30 12:56:28,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (32) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/32/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/32/galaxy_32.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:56:28,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:56:28,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10: mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:56:28,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:56:55,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 32: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:57:01,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 32 finished +galaxy.model.metadata DEBUG 2024-08-30 12:57:01,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 43 +galaxy.model.metadata DEBUG 2024-08-30 12:57:01,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 41 +galaxy.model.metadata DEBUG 2024-08-30 12:57:01,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 42 +galaxy.util WARNING 2024-08-30 12:57:01,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/0/7/6/dataset_0769d0b8-f60d-4d5d-94da-f071cb821c26.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/0/7/6/dataset_0769d0b8-f60d-4d5d-94da-f071cb821c26.dat' +galaxy.util WARNING 2024-08-30 12:57:01,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/d/8/a/dataset_d8aa9ded-1390-495a-9a76-aa639af0d205.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/d/8/a/dataset_d8aa9ded-1390-495a-9a76-aa639af0d205.dat' +galaxy.jobs INFO 2024-08-30 12:57:01,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 32 in /galaxy/server/database/jobs_directory/000/32 +galaxy.objectstore CRITICAL 2024-08-30 12:57:01,291 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'plot.test.py' +galaxy.jobs DEBUG 2024-08-30 12:57:01,291 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 32 executed (199.126 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:57:03,484 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 33 +tpv.core.entities DEBUG 2024-08-30 12:57:03,521 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:57:03,521 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:57:03,525 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:57:03,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:57:03,561 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Working directory for job is: /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs.runners DEBUG 2024-08-30 12:57:03,569 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [33] queued (43.433 ms) +galaxy.jobs.handler INFO 2024-08-30 12:57:03,573 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:57:03,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 33 +galaxy.jobs DEBUG 2024-08-30 12:57:03,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [33] prepared (98.127 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:57:03,726 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/33/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/33/registry.xml' '/galaxy/server/database/jobs_directory/000/33/upload_params.json' '44:/galaxy/server/database/objects/8/a/5/dataset_8a5edff4-5721-4aee-b148-fed33af01781_files:/galaxy/server/database/objects/8/a/5/dataset_8a5edff4-5721-4aee-b148-fed33af01781.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:57:03,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (33) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/33/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/33/galaxy_33.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:57:11,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 33: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:57:17,106 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 33 finished +galaxy.model.metadata DEBUG 2024-08-30 12:57:17,170 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 44 +galaxy.jobs INFO 2024-08-30 12:57:17,210 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 33 in /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs DEBUG 2024-08-30 12:57:17,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 33 executed (135.711 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:57:17,913 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 34 +tpv.core.entities DEBUG 2024-08-30 12:57:17,950 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:57:17,951 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:57:17,956 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:57:17,974 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:57:17,999 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Working directory for job is: /galaxy/server/database/jobs_directory/000/34 +galaxy.jobs.runners DEBUG 2024-08-30 12:57:18,008 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [34] queued (51.624 ms) +galaxy.jobs.handler INFO 2024-08-30 12:57:18,012 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:57:18,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 34 +galaxy.jobs DEBUG 2024-08-30 12:57:18,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [34] prepared (63.891 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:57:18,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:57:18,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10: mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:57:18,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:57:18,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/34/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/34/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/a/5/dataset_8a5edff4-5721-4aee-b148-fed33af01781.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp --aberrant "1.0,1.0" --BAF-weight 1.0 --BAF-dev "0.04,0.04" --LRR-weight 0.2 --LRR-dev "0.2,0.2" --LRR-smooth-win 10 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/d/3/b/dataset_d3bf143f-6240-4646-80a1-007581f820b9.dat' && mv cnv_tmp/summary.*.tab '/galaxy/server/database/objects/1/c/c/dataset_1cc76856-26db-4b2d-931d-d15cd53421ee.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:57:18,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (34) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/34/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/34/galaxy_34.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:57:18,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:57:18,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10: mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:57:18,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:57:23,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 34: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:57:28,166 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 34 finished +galaxy.model.metadata DEBUG 2024-08-30 12:57:28,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 45 +galaxy.model.metadata DEBUG 2024-08-30 12:57:28,240 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 46 +galaxy.util WARNING 2024-08-30 12:57:28,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/d/3/b/dataset_d3bf143f-6240-4646-80a1-007581f820b9.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/d/3/b/dataset_d3bf143f-6240-4646-80a1-007581f820b9.dat' +galaxy.util WARNING 2024-08-30 12:57:28,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/1/c/c/dataset_1cc76856-26db-4b2d-931d-d15cd53421ee.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/1/c/c/dataset_1cc76856-26db-4b2d-931d-d15cd53421ee.dat' +galaxy.jobs INFO 2024-08-30 12:57:28,279 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 34 in /galaxy/server/database/jobs_directory/000/34 +galaxy.objectstore CRITICAL 2024-08-30 12:57:28,334 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'plot.test.py' +galaxy.jobs DEBUG 2024-08-30 12:57:28,334 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 34 executed (136.669 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:57:30,385 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 35 +tpv.core.entities DEBUG 2024-08-30 12:57:30,417 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:57:30,417 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:57:30,423 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:57:30,440 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:57:30,459 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Working directory for job is: /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs.runners DEBUG 2024-08-30 12:57:30,468 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [35] queued (44.716 ms) +galaxy.jobs.handler INFO 2024-08-30 12:57:30,472 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:57:30,478 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 35 +galaxy.jobs DEBUG 2024-08-30 12:57:30,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [35] prepared (105.605 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:57:30,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/35/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/35/registry.xml' '/galaxy/server/database/jobs_directory/000/35/upload_params.json' '47:/galaxy/server/database/objects/4/f/d/dataset_4fd6a427-8363-42f8-8067-838469bfbf0a_files:/galaxy/server/database/objects/4/f/d/dataset_4fd6a427-8363-42f8-8067-838469bfbf0a.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:57:30,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (35) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/35/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/35/galaxy_35.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:57:39,272 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 35: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:57:44,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 35 finished +galaxy.model.metadata DEBUG 2024-08-30 12:57:44,511 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 47 +galaxy.jobs INFO 2024-08-30 12:57:44,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 35 in /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs DEBUG 2024-08-30 12:57:44,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 35 executed (159.290 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:57:45,825 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 36 +tpv.core.entities DEBUG 2024-08-30 12:57:45,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:57:45,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:57:45,877 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:57:45,897 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:57:45,924 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Working directory for job is: /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs.runners DEBUG 2024-08-30 12:57:45,932 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [36] queued (55.251 ms) +galaxy.jobs.handler INFO 2024-08-30 12:57:45,936 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:57:45,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 36 +galaxy.jobs DEBUG 2024-08-30 12:57:46,036 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [36] prepared (78.846 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:57:46,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:57:46,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10: mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:57:46,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:57:46,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/36/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/36/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/f/d/dataset_4fd6a427-8363-42f8-8067-838469bfbf0a.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp -c 'test' -s 'test' -p 0 --aberrant "1.0,1.0" --BAF-weight 1.0 --BAF-dev "0.04,0.04" --LRR-weight 0.2 --LRR-dev "0.2,0.2" --LRR-smooth-win 10 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/9/a/a/dataset_9aab51e9-e62d-45b3-9601-d81a62dbe528.dat' && mv cnv_tmp/summary.tab '/galaxy/server/database/objects/a/1/c/dataset_a1c47531-bbb4-42b2-8b85-4b3d651a867a.dat' && (echo 'Copy-number variation plots (bcftools cnv)' > /galaxy/server/database/objects/9/8/7/dataset_98793b8d-c28b-4266-8acf-e51f3d920cc0.dat; for plot in cnv_tmp/*.png; do [ -f "$plot" ] || break; echo '
' >> /galaxy/server/database/objects/9/8/7/dataset_98793b8d-c28b-4266-8acf-e51f3d920cc0.dat; done; echo '' >> /galaxy/server/database/objects/9/8/7/dataset_98793b8d-c28b-4266-8acf-e51f3d920cc0.dat;)] +galaxy.jobs.runners DEBUG 2024-08-30 12:57:46,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (36) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/36/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/36/galaxy_36.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:57:46,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:57:46,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10: mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:57:46,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:57:54,526 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 36: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:57:59,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 36 finished +galaxy.model.metadata DEBUG 2024-08-30 12:57:59,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 50 +galaxy.model.metadata DEBUG 2024-08-30 12:57:59,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 48 +galaxy.model.metadata DEBUG 2024-08-30 12:57:59,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 49 +galaxy.util WARNING 2024-08-30 12:57:59,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/a/a/dataset_9aab51e9-e62d-45b3-9601-d81a62dbe528.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/a/a/dataset_9aab51e9-e62d-45b3-9601-d81a62dbe528.dat' +galaxy.util WARNING 2024-08-30 12:57:59,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/a/1/c/dataset_a1c47531-bbb4-42b2-8b85-4b3d651a867a.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/1/c/dataset_a1c47531-bbb4-42b2-8b85-4b3d651a867a.dat' +galaxy.jobs INFO 2024-08-30 12:57:59,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 36 in /galaxy/server/database/jobs_directory/000/36 +galaxy.objectstore CRITICAL 2024-08-30 12:57:59,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'plot.test.test.py' +galaxy.jobs DEBUG 2024-08-30 12:57:59,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 36 executed (176.861 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:58:02,316 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 37 +tpv.core.entities DEBUG 2024-08-30 12:58:02,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:58:02,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:58:02,363 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:58:02,380 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:58:02,401 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Working directory for job is: /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs.runners DEBUG 2024-08-30 12:58:02,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [37] queued (45.932 ms) +galaxy.jobs.handler INFO 2024-08-30 12:58:02,413 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:58:02,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 37 +galaxy.jobs DEBUG 2024-08-30 12:58:02,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [37] prepared (107.345 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:58:02,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/37/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/37/registry.xml' '/galaxy/server/database/jobs_directory/000/37/upload_params.json' '51:/galaxy/server/database/objects/a/5/f/dataset_a5f78e95-6f79-49dc-b010-352d9e643601_files:/galaxy/server/database/objects/a/5/f/dataset_a5f78e95-6f79-49dc-b010-352d9e643601.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:58:02,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (37) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/37/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/37/galaxy_37.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:58:10,658 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 37: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:58:15,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 37 finished +galaxy.model.metadata DEBUG 2024-08-30 12:58:15,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 51 +galaxy.jobs INFO 2024-08-30 12:58:15,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 37 in /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs DEBUG 2024-08-30 12:58:15,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 37 executed (153.683 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:58:16,884 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 38 +tpv.core.entities DEBUG 2024-08-30 12:58:16,927 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:58:16,928 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:58:16,934 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:58:16,954 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:58:16,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Working directory for job is: /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs.runners DEBUG 2024-08-30 12:58:16,991 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [38] queued (56.549 ms) +galaxy.jobs.handler INFO 2024-08-30 12:58:16,997 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:58:16,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 38 +galaxy.jobs DEBUG 2024-08-30 12:58:17,092 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [38] prepared (72.539 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:58:17,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:58:17,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10: mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:58:17,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:58:17,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/38/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/38/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/a/5/f/dataset_a5f78e95-6f79-49dc-b010-352d9e643601.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp --aberrant "1.0,1.0" --BAF-weight 1 --BAF-dev "0.04,0.04" --LRR-weight 0 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/b/4/a/dataset_b4ac5087-c77a-4095-ade6-6187f6f3c15d.dat' && mv cnv_tmp/summary.*.tab '/galaxy/server/database/objects/c/8/4/dataset_c840bf3a-243c-4a67-a099-8c4d772e01e3.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:58:17,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (38) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/38/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/38/galaxy_38.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:58:17,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:58:17,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10: mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:58:17,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-3f0b2099bce3ecb75064dfe6cdabcd4018727aa8:4d401db796b250450884561726017d2d1e3a0333-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:58:22,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 38: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:58:28,001 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 38 finished +galaxy.model.metadata DEBUG 2024-08-30 12:58:28,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 52 +galaxy.model.metadata DEBUG 2024-08-30 12:58:28,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 53 +galaxy.util WARNING 2024-08-30 12:58:28,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/b/4/a/dataset_b4ac5087-c77a-4095-ade6-6187f6f3c15d.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/b/4/a/dataset_b4ac5087-c77a-4095-ade6-6187f6f3c15d.dat' +galaxy.util WARNING 2024-08-30 12:58:28,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/8/4/dataset_c840bf3a-243c-4a67-a099-8c4d772e01e3.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/8/4/dataset_c840bf3a-243c-4a67-a099-8c4d772e01e3.dat' +galaxy.jobs INFO 2024-08-30 12:58:28,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 38 in /galaxy/server/database/jobs_directory/000/38 +galaxy.objectstore CRITICAL 2024-08-30 12:58:28,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'plot.test.py' +galaxy.jobs DEBUG 2024-08-30 12:58:28,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 38 executed (178.411 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:58:32,347 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 39 +tpv.core.entities DEBUG 2024-08-30 12:58:32,381 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:58:32,382 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:58:32,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:58:32,402 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:58:32,422 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Working directory for job is: /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs.runners DEBUG 2024-08-30 12:58:32,430 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [39] queued (43.541 ms) +galaxy.jobs.handler INFO 2024-08-30 12:58:32,433 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:58:32,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 39 +galaxy.jobs DEBUG 2024-08-30 12:58:32,563 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [39] prepared (102.015 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:58:32,592 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/39/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/39/registry.xml' '/galaxy/server/database/jobs_directory/000/39/upload_params.json' '54:/galaxy/server/database/objects/9/0/e/dataset_90e25232-e913-4060-a42e-b369ccbf38a1_files:/galaxy/server/database/objects/9/0/e/dataset_90e25232-e913-4060-a42e-b369ccbf38a1.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:58:32,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (39) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/39/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/39/galaxy_39.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:58:40,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 39: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:58:46,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 39 finished +galaxy.model.metadata DEBUG 2024-08-30 12:58:46,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 54 +galaxy.jobs INFO 2024-08-30 12:58:46,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 39 in /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs DEBUG 2024-08-30 12:58:46,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 39 executed (130.700 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:58:47,762 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 40 +tpv.core.entities DEBUG 2024-08-30 12:58:47,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:58:47,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:58:47,806 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:58:47,822 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:58:47,841 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Working directory for job is: /galaxy/server/database/jobs_directory/000/40 +galaxy.jobs.runners DEBUG 2024-08-30 12:58:47,849 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [40] queued (43.303 ms) +galaxy.jobs.handler INFO 2024-08-30 12:58:47,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:58:47,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 40 +galaxy.jobs DEBUG 2024-08-30 12:58:47,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [40] prepared (96.834 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:58:47,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:58:47,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:58:48,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:58:48,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/40/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/40/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/9/0/e/dataset_90e25232-e913-4060-a42e-b369ccbf38a1.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools roh --AF-dflt "0.4" --GTs-only "30.0" --hw-to-az "6.7e-08" --az-to-hw "5e-09" input.vcf.gz > '/galaxy/server/database/objects/9/1/6/dataset_91661122-93ee-4b77-a728-da66819db87b.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:58:48,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (40) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/40/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/40/galaxy_40.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:58:48,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:58:48,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:58:48,240 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:58:58,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 40: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:59:03,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 40 finished +galaxy.model.metadata DEBUG 2024-08-30 12:59:03,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 55 +galaxy.jobs INFO 2024-08-30 12:59:03,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 40 in /galaxy/server/database/jobs_directory/000/40 +galaxy.jobs DEBUG 2024-08-30 12:59:03,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 40 executed (151.967 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:59:07,331 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 41 +tpv.core.entities DEBUG 2024-08-30 12:59:07,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:59:07,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:59:07,377 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:59:07,394 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:59:07,417 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Working directory for job is: /galaxy/server/database/jobs_directory/000/41 +galaxy.jobs.runners DEBUG 2024-08-30 12:59:07,426 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [41] queued (49.094 ms) +galaxy.jobs.handler INFO 2024-08-30 12:59:07,430 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:59:07,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 41 +galaxy.jobs DEBUG 2024-08-30 12:59:07,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [41] prepared (107.991 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:59:07,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/41/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/41/registry.xml' '/galaxy/server/database/jobs_directory/000/41/upload_params.json' '56:/galaxy/server/database/objects/a/0/9/dataset_a092ad03-0b78-4e9e-8237-00748efe3dc8_files:/galaxy/server/database/objects/a/0/9/dataset_a092ad03-0b78-4e9e-8237-00748efe3dc8.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:59:07,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (41) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/41/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/41/galaxy_41.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:59:15,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 41: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:59:20,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 41 finished +galaxy.model.metadata DEBUG 2024-08-30 12:59:20,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 56 +galaxy.jobs INFO 2024-08-30 12:59:20,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 41 in /galaxy/server/database/jobs_directory/000/41 +galaxy.jobs DEBUG 2024-08-30 12:59:21,040 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 41 executed (149.084 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:59:21,881 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 42 +tpv.core.entities DEBUG 2024-08-30 12:59:21,916 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:59:21,916 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:59:21,921 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:59:21,937 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:59:21,956 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Working directory for job is: /galaxy/server/database/jobs_directory/000/42 +galaxy.jobs.runners DEBUG 2024-08-30 12:59:21,965 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [42] queued (43.838 ms) +galaxy.jobs.handler INFO 2024-08-30 12:59:21,969 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:59:21,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 42 +galaxy.jobs DEBUG 2024-08-30 12:59:22,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [42] prepared (70.413 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:59:22,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:59:22,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:59:22,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:59:22,115 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/42/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/42/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/a/0/9/dataset_a092ad03-0b78-4e9e-8237-00748efe3dc8.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools roh --AF-dflt "0.4" --GTs-only "30.0" --hw-to-az "6.7e-08" --az-to-hw "5e-09" --output-type r input.vcf.gz > '/galaxy/server/database/objects/a/b/0/dataset_ab0c362c-9692-4519-932e-dad2c0b4f998.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:59:22,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (42) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/42/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/42/galaxy_42.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:59:22,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:59:22,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:59:22,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 12:59:27,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 42: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:59:32,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 42 finished +galaxy.model.metadata DEBUG 2024-08-30 12:59:32,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 57 +galaxy.jobs INFO 2024-08-30 12:59:32,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 42 in /galaxy/server/database/jobs_directory/000/42 +galaxy.jobs DEBUG 2024-08-30 12:59:32,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 42 executed (147.391 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:59:36,285 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 43 +tpv.core.entities DEBUG 2024-08-30 12:59:36,319 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:59:36,320 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:59:36,325 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:59:36,342 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:59:36,363 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Working directory for job is: /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs.runners DEBUG 2024-08-30 12:59:36,373 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [43] queued (47.819 ms) +galaxy.jobs.handler INFO 2024-08-30 12:59:36,377 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:59:36,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 43 +galaxy.jobs DEBUG 2024-08-30 12:59:36,502 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [43] prepared (98.676 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:59:36,529 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/43/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/43/registry.xml' '/galaxy/server/database/jobs_directory/000/43/upload_params.json' '58:/galaxy/server/database/objects/a/6/f/dataset_a6f72704-c648-4565-a679-1824a5039d9c_files:/galaxy/server/database/objects/a/6/f/dataset_a6f72704-c648-4565-a679-1824a5039d9c.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:59:36,544 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (43) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/43/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/43/galaxy_43.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-08-30 12:59:37,380 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 44 +tpv.core.entities DEBUG 2024-08-30 12:59:37,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:59:37,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:59:37,424 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:59:37,444 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:59:37,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Working directory for job is: /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs.runners DEBUG 2024-08-30 12:59:37,475 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [44] queued (50.695 ms) +galaxy.jobs.handler INFO 2024-08-30 12:59:37,478 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:59:37,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 44 +galaxy.jobs DEBUG 2024-08-30 12:59:37,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [44] prepared (99.255 ms) +galaxy.jobs.command_factory INFO 2024-08-30 12:59:37,629 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/44/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/44/registry.xml' '/galaxy/server/database/jobs_directory/000/44/upload_params.json' '59:/galaxy/server/database/objects/c/0/c/dataset_c0cb62bc-d241-470a-92c2-09bf6e325b65_files:/galaxy/server/database/objects/c/0/c/dataset_c0cb62bc-d241-470a-92c2-09bf6e325b65.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:59:37,647 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (44) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/44/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/44/galaxy_44.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 12:59:45,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 43: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:59:46,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 44: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 12:59:50,848 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 43 finished +galaxy.model.metadata DEBUG 2024-08-30 12:59:50,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 58 +galaxy.jobs INFO 2024-08-30 12:59:50,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 43 in /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs DEBUG 2024-08-30 12:59:51,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 43 executed (149.768 ms) +galaxy.jobs.runners DEBUG 2024-08-30 12:59:51,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 44 finished +galaxy.model.metadata DEBUG 2024-08-30 12:59:51,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 59 +galaxy.jobs INFO 2024-08-30 12:59:51,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 44 in /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs DEBUG 2024-08-30 12:59:51,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 44 executed (166.356 ms) +galaxy.jobs.handler DEBUG 2024-08-30 12:59:52,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 45 +tpv.core.entities DEBUG 2024-08-30 12:59:52,947 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 12:59:52,947 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 12:59:52,955 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 12:59:52,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 12:59:53,002 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Working directory for job is: /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs.runners DEBUG 2024-08-30 12:59:53,013 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [45] queued (57.795 ms) +galaxy.jobs.handler INFO 2024-08-30 12:59:53,017 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 12:59:53,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 45 +galaxy.jobs DEBUG 2024-08-30 12:59:53,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [45] prepared (76.010 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 12:59:53,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:59:53,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:59:53,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 12:59:53,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/45/tool_script.sh] for tool command [vcfintersect -b '/galaxy/server/database/objects/c/0/c/dataset_c0cb62bc-d241-470a-92c2-09bf6e325b65.dat' '/galaxy/server/database/objects/a/6/f/dataset_a6f72704-c648-4565-a679-1824a5039d9c.dat' > '/galaxy/server/database/objects/5/1/7/dataset_5171451e-a406-43d5-ad38-f8630cf9bd2d.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 12:59:53,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (45) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/45/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/45/galaxy_45.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 12:59:53,383 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 12:59:53,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-08-30 12:59:53,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:00:03,025 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 45: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:00:08,313 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 45 finished +galaxy.model.metadata DEBUG 2024-08-30 13:00:08,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 60 +galaxy.jobs INFO 2024-08-30 13:00:08,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 45 in /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs DEBUG 2024-08-30 13:00:08,498 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 45 executed (155.452 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:00:11,475 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 46 +tpv.core.entities DEBUG 2024-08-30 13:00:11,513 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:00:11,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:00:11,520 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:00:11,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:00:11,558 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Working directory for job is: /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs.runners DEBUG 2024-08-30 13:00:11,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [46] queued (46.845 ms) +galaxy.jobs.handler INFO 2024-08-30 13:00:11,571 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:00:11,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 46 +galaxy.jobs DEBUG 2024-08-30 13:00:11,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [46] prepared (108.010 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:00:11,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/46/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/46/registry.xml' '/galaxy/server/database/jobs_directory/000/46/upload_params.json' '61:/galaxy/server/database/objects/d/2/3/dataset_d2340288-58bf-408b-bf0f-14d66a7eaa8f_files:/galaxy/server/database/objects/d/2/3/dataset_d2340288-58bf-408b-bf0f-14d66a7eaa8f.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:00:11,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (46) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/46/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/46/galaxy_46.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:00:20,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 46: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:00:25,383 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 46 finished +galaxy.model.metadata DEBUG 2024-08-30 13:00:25,455 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 61 +galaxy.jobs INFO 2024-08-30 13:00:25,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 46 in /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs DEBUG 2024-08-30 13:00:25,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 46 executed (153.629 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:00:26,942 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 47 +tpv.core.entities DEBUG 2024-08-30 13:00:26,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:00:26,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:00:26,987 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:00:27,006 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:00:27,026 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Working directory for job is: /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs.runners DEBUG 2024-08-30 13:00:27,036 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [47] queued (48.876 ms) +galaxy.jobs.handler INFO 2024-08-30 13:00:27,040 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:00:27,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 47 +galaxy.jobs DEBUG 2024-08-30 13:00:27,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [47] prepared (69.767 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:00:27,134 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:00:27,134 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:00:27,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:00:27,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/47/tool_script.sh] for tool command [vcfintersect -R '20:1-30000' '/galaxy/server/database/objects/d/2/3/dataset_d2340288-58bf-408b-bf0f-14d66a7eaa8f.dat' > '/galaxy/server/database/objects/8/8/a/dataset_88a227fe-e761-4aab-9de1-8ee984b95784.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:00:27,197 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (47) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/47/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/47/galaxy_47.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:00:27,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:00:27,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:00:27,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:00:31,424 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 47: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:00:36,545 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 47 finished +galaxy.model.metadata DEBUG 2024-08-30 13:00:36,622 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 62 +galaxy.jobs INFO 2024-08-30 13:00:36,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 47 in /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs DEBUG 2024-08-30 13:00:36,724 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 47 executed (146.466 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:00:40,353 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 48 +tpv.core.entities DEBUG 2024-08-30 13:00:40,391 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:00:40,392 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:00:40,397 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:00:40,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:00:40,439 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Working directory for job is: /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs.runners DEBUG 2024-08-30 13:00:40,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [48] queued (49.313 ms) +galaxy.jobs.handler INFO 2024-08-30 13:00:40,451 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:00:40,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 48 +galaxy.jobs DEBUG 2024-08-30 13:00:40,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [48] prepared (116.222 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:00:40,627 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/48/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/48/registry.xml' '/galaxy/server/database/jobs_directory/000/48/upload_params.json' '63:/galaxy/server/database/objects/d/3/a/dataset_d3a34ff3-1282-413a-ac33-853dc82f65a5_files:/galaxy/server/database/objects/d/3/a/dataset_d3a34ff3-1282-413a-ac33-853dc82f65a5.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:00:40,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (48) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/48/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/48/galaxy_48.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-08-30 13:00:41,454 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 49, 50 +tpv.core.entities DEBUG 2024-08-30 13:00:41,492 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:00:41,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:00:41,497 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:00:41,516 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:00:41,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Working directory for job is: /galaxy/server/database/jobs_directory/000/49 +galaxy.jobs.runners DEBUG 2024-08-30 13:00:41,545 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [49] queued (47.579 ms) +galaxy.jobs.handler INFO 2024-08-30 13:00:41,550 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:00:41,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 49 +tpv.core.entities DEBUG 2024-08-30 13:00:41,575 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:00:41,575 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:00:41,585 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:00:41,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:00:41,653 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Working directory for job is: /galaxy/server/database/jobs_directory/000/50 +galaxy.jobs.runners DEBUG 2024-08-30 13:00:41,663 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [50] queued (77.311 ms) +galaxy.jobs.handler INFO 2024-08-30 13:00:41,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:00:41,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 50 +galaxy.jobs DEBUG 2024-08-30 13:00:41,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [49] prepared (137.661 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:00:41,764 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/49/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/49/registry.xml' '/galaxy/server/database/jobs_directory/000/49/upload_params.json' '64:/galaxy/server/database/objects/1/9/4/dataset_194c884f-2c23-4f23-9110-28dfeeb81ea5_files:/galaxy/server/database/objects/1/9/4/dataset_194c884f-2c23-4f23-9110-28dfeeb81ea5.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:00:41,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (49) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/49/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/49/galaxy_49.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-08-30 13:00:41,832 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [50] prepared (126.295 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:00:41,860 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/50/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/50/registry.xml' '/galaxy/server/database/jobs_directory/000/50/upload_params.json' '65:/galaxy/server/database/objects/9/2/7/dataset_9272632b-1675-4e45-bd91-d5af269cd9b0_files:/galaxy/server/database/objects/9/2/7/dataset_9272632b-1675-4e45-bd91-d5af269cd9b0.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:00:41,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (50) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/50/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/50/galaxy_50.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:00:50,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 48: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:00:50,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 49: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:00:51,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 50: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:00:57,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 48 finished +galaxy.model.metadata DEBUG 2024-08-30 13:00:57,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 63 +galaxy.jobs INFO 2024-08-30 13:00:57,872 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 48 in /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs DEBUG 2024-08-30 13:00:57,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 48 executed (161.072 ms) +galaxy.jobs.runners DEBUG 2024-08-30 13:00:57,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 49 finished +galaxy.model.metadata DEBUG 2024-08-30 13:00:58,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 64 +galaxy.jobs INFO 2024-08-30 13:00:58,057 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 49 in /galaxy/server/database/jobs_directory/000/49 +galaxy.jobs DEBUG 2024-08-30 13:00:58,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 49 executed (144.464 ms) +galaxy.jobs.runners DEBUG 2024-08-30 13:00:58,789 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 50 finished +galaxy.model.metadata DEBUG 2024-08-30 13:00:58,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 65 +galaxy.jobs INFO 2024-08-30 13:00:58,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 50 in /galaxy/server/database/jobs_directory/000/50 +galaxy.jobs DEBUG 2024-08-30 13:00:58,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 50 executed (145.239 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:01:00,316 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 51 +tpv.core.entities DEBUG 2024-08-30 13:01:00,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:01:00,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:01:00,377 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:01:00,395 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:01:00,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Working directory for job is: /galaxy/server/database/jobs_directory/000/51 +galaxy.jobs.runners DEBUG 2024-08-30 13:01:00,428 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [51] queued (51.574 ms) +galaxy.jobs.handler INFO 2024-08-30 13:01:00,434 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:01:00,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 51 +galaxy.jobs DEBUG 2024-08-30 13:01:00,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [51] prepared (72.505 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:01:00,529 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:01:00,529 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:01:00,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:01:00,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/51/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/9/2/7/dataset_9272632b-1675-4e45-bd91-d5af269cd9b0.dat' 'localref.fa' && vcfintersect -r 'localref.fa' -w "30" -i '/galaxy/server/database/objects/d/3/a/dataset_d3a34ff3-1282-413a-ac33-853dc82f65a5.dat' '/galaxy/server/database/objects/1/9/4/dataset_194c884f-2c23-4f23-9110-28dfeeb81ea5.dat' > '/galaxy/server/database/objects/8/0/3/dataset_803ffafe-159b-4252-9e8a-4826ed1772b1.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:01:00,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (51) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/51/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/51/galaxy_51.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:01:00,612 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:01:00,612 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:01:00,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:01:05,402 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 51: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:01:10,410 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 51 finished +galaxy.model.metadata DEBUG 2024-08-30 13:01:10,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 66 +galaxy.jobs INFO 2024-08-30 13:01:10,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 51 in /galaxy/server/database/jobs_directory/000/51 +galaxy.jobs DEBUG 2024-08-30 13:01:10,594 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 51 executed (153.046 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:01:12,734 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 52 +tpv.core.entities DEBUG 2024-08-30 13:01:12,775 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:01:12,775 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:01:12,781 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:01:12,802 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:01:12,825 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Working directory for job is: /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs.runners DEBUG 2024-08-30 13:01:12,833 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [52] queued (51.435 ms) +galaxy.jobs.handler INFO 2024-08-30 13:01:12,837 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:01:12,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 52 +galaxy.jobs DEBUG 2024-08-30 13:01:12,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [52] prepared (108.813 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:01:13,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/52/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/52/registry.xml' '/galaxy/server/database/jobs_directory/000/52/upload_params.json' '67:/galaxy/server/database/objects/d/d/9/dataset_dd971fd5-70d5-4519-81de-794fbaf69ba0_files:/galaxy/server/database/objects/d/d/9/dataset_dd971fd5-70d5-4519-81de-794fbaf69ba0.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:01:13,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (52) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/52/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/52/galaxy_52.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-08-30 13:01:13,841 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 54, 53 +tpv.core.entities DEBUG 2024-08-30 13:01:13,892 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:01:13,893 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:01:13,899 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:01:13,917 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:01:13,938 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Working directory for job is: /galaxy/server/database/jobs_directory/000/53 +galaxy.jobs.runners DEBUG 2024-08-30 13:01:13,945 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [53] queued (45.792 ms) +galaxy.jobs.handler INFO 2024-08-30 13:01:13,949 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:01:13,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 53 +tpv.core.entities DEBUG 2024-08-30 13:01:13,967 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:01:13,968 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:01:13,974 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:01:13,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:01:14,035 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Working directory for job is: /galaxy/server/database/jobs_directory/000/54 +galaxy.jobs.runners DEBUG 2024-08-30 13:01:14,046 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [54] queued (72.220 ms) +galaxy.jobs.handler INFO 2024-08-30 13:01:14,052 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:01:14,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 54 +galaxy.jobs DEBUG 2024-08-30 13:01:14,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [53] prepared (123.169 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:01:14,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/53/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/53/registry.xml' '/galaxy/server/database/jobs_directory/000/53/upload_params.json' '68:/galaxy/server/database/objects/4/5/7/dataset_45765b05-9215-41e2-9a75-66f75bc720a7_files:/galaxy/server/database/objects/4/5/7/dataset_45765b05-9215-41e2-9a75-66f75bc720a7.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:01:14,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (53) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/53/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/53/galaxy_53.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-08-30 13:01:14,211 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [54] prepared (130.294 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:01:14,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/54/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/54/registry.xml' '/galaxy/server/database/jobs_directory/000/54/upload_params.json' '69:/galaxy/server/database/objects/9/3/a/dataset_93a8e8f5-0f0b-43b0-a07f-a29e3900a1c8_files:/galaxy/server/database/objects/9/3/a/dataset_93a8e8f5-0f0b-43b0-a07f-a29e3900a1c8.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:01:14,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (54) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/54/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/54/galaxy_54.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:01:21,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 52: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:01:23,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 54: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:01:23,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 53: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:01:29,611 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 52 finished +galaxy.model.metadata DEBUG 2024-08-30 13:01:29,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 67 +galaxy.jobs INFO 2024-08-30 13:01:29,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 52 in /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs DEBUG 2024-08-30 13:01:29,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 52 executed (156.547 ms) +galaxy.jobs.runners DEBUG 2024-08-30 13:01:30,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 53 finished +galaxy.jobs.runners DEBUG 2024-08-30 13:01:30,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 54 finished +galaxy.model.metadata DEBUG 2024-08-30 13:01:30,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 68 +galaxy.jobs INFO 2024-08-30 13:01:30,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 53 in /galaxy/server/database/jobs_directory/000/53 +galaxy.model.metadata DEBUG 2024-08-30 13:01:30,857 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 69 +galaxy.jobs INFO 2024-08-30 13:01:30,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 54 in /galaxy/server/database/jobs_directory/000/54 +galaxy.jobs DEBUG 2024-08-30 13:01:30,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 53 executed (176.814 ms) +galaxy.jobs DEBUG 2024-08-30 13:01:30,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 54 executed (156.752 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:01:31,631 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 55 +tpv.core.entities DEBUG 2024-08-30 13:01:31,681 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:01:31,682 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:01:31,688 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:01:31,709 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:01:31,733 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Working directory for job is: /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs.runners DEBUG 2024-08-30 13:01:31,745 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [55] queued (57.018 ms) +galaxy.jobs.handler INFO 2024-08-30 13:01:31,751 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:01:31,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 55 +galaxy.jobs DEBUG 2024-08-30 13:01:31,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [55] prepared (96.617 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:01:31,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:01:31,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:01:31,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:01:31,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/55/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/9/3/a/dataset_93a8e8f5-0f0b-43b0-a07f-a29e3900a1c8.dat' 'localref.fa' && vcfintersect -r 'localref.fa' -w "30" -u '/galaxy/server/database/objects/d/d/9/dataset_dd971fd5-70d5-4519-81de-794fbaf69ba0.dat' '/galaxy/server/database/objects/4/5/7/dataset_45765b05-9215-41e2-9a75-66f75bc720a7.dat' > '/galaxy/server/database/objects/d/b/e/dataset_dbe5b312-3bc6-4567-b354-f0ec5bc88527.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:01:31,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (55) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/55/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/55/galaxy_55.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:01:31,970 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:01:31,970 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:01:31,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:01:36,187 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 55: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:01:41,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 55 finished +galaxy.model.metadata DEBUG 2024-08-30 13:01:41,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 70 +galaxy.jobs INFO 2024-08-30 13:01:41,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 55 in /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs DEBUG 2024-08-30 13:01:41,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 55 executed (162.951 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:01:46,110 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 56 +tpv.core.entities DEBUG 2024-08-30 13:01:46,158 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:01:46,159 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:01:46,165 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:01:46,187 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:01:46,212 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Working directory for job is: /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs.runners DEBUG 2024-08-30 13:01:46,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [56] queued (57.119 ms) +galaxy.jobs.handler INFO 2024-08-30 13:01:46,227 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:01:46,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 56 +galaxy.jobs DEBUG 2024-08-30 13:01:46,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [56] prepared (114.663 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:01:46,402 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/56/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/56/registry.xml' '/galaxy/server/database/jobs_directory/000/56/upload_params.json' '71:/galaxy/server/database/objects/a/4/7/dataset_a473f856-9874-432a-af38-cb4c9b776d2b_files:/galaxy/server/database/objects/a/4/7/dataset_a473f856-9874-432a-af38-cb4c9b776d2b.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:01:46,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (56) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/56/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/56/galaxy_56.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:01:55,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 56: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:02:00,622 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 56 finished +galaxy.model.metadata DEBUG 2024-08-30 13:02:00,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 71 +galaxy.jobs INFO 2024-08-30 13:02:00,738 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 56 in /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs DEBUG 2024-08-30 13:02:00,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 56 executed (148.731 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:02:01,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 57 +tpv.core.entities DEBUG 2024-08-30 13:02:01,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/.*, abstract=False, cores=1, mem=11.4, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:02:01,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:02:01,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:02:01,673 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:02:01,691 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Working directory for job is: /galaxy/server/database/jobs_directory/000/57 +galaxy.jobs.runners DEBUG 2024-08-30 13:02:01,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [57] queued (45.851 ms) +galaxy.jobs.handler INFO 2024-08-30 13:02:01,706 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:02:01,711 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 57 +galaxy.jobs DEBUG 2024-08-30 13:02:01,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [57] prepared (64.660 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:02:01,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:02:01,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:02:01,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:02:02,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/57/tool_script.sh] for tool command [export MPLBACKEND="agg" && poretools hist '/galaxy/server/database/objects/a/4/7/dataset_a473f856-9874-432a-af38-cb4c9b776d2b.dat' --saveas histogram.png --min-length 0 --max-length 1000000000 --num-bins 50 && mv histogram.png '/galaxy/server/database/objects/3/9/4/dataset_3945699f-1e5b-4f38-8b2b-37f4ac938d4c.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:02:02,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (57) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/57/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/57/galaxy_57.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:02:02,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:02:02,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:02:02,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:02:29,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 57: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:02:35,063 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 57 finished +galaxy.model.metadata DEBUG 2024-08-30 13:02:35,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 72 +galaxy.util WARNING 2024-08-30 13:02:35,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/9/4/dataset_3945699f-1e5b-4f38-8b2b-37f4ac938d4c.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/9/4/dataset_3945699f-1e5b-4f38-8b2b-37f4ac938d4c.dat' +galaxy.jobs INFO 2024-08-30 13:02:35,188 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 57 in /galaxy/server/database/jobs_directory/000/57 +galaxy.jobs DEBUG 2024-08-30 13:02:35,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 57 executed (162.055 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:02:38,607 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 58 +tpv.core.entities DEBUG 2024-08-30 13:02:38,643 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:02:38,643 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:02:38,648 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:02:38,665 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:02:38,686 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Working directory for job is: /galaxy/server/database/jobs_directory/000/58 +galaxy.jobs.runners DEBUG 2024-08-30 13:02:38,694 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [58] queued (45.664 ms) +galaxy.jobs.handler INFO 2024-08-30 13:02:38,698 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:02:38,703 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 58 +galaxy.jobs DEBUG 2024-08-30 13:02:38,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [58] prepared (116.259 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:02:38,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/58/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/58/registry.xml' '/galaxy/server/database/jobs_directory/000/58/upload_params.json' '73:/galaxy/server/database/objects/3/1/4/dataset_31467151-7d33-4d0c-a100-9ed18f2b85be_files:/galaxy/server/database/objects/3/1/4/dataset_31467151-7d33-4d0c-a100-9ed18f2b85be.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:02:38,890 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (58) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/58/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/58/galaxy_58.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:02:47,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 58: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:02:52,533 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 58 finished +galaxy.model.metadata DEBUG 2024-08-30 13:02:52,611 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 73 +galaxy.jobs INFO 2024-08-30 13:02:52,658 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 58 in /galaxy/server/database/jobs_directory/000/58 +galaxy.jobs DEBUG 2024-08-30 13:02:52,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 58 executed (163.928 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:02:53,032 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 59 +tpv.core.entities DEBUG 2024-08-30 13:02:53,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/.*, abstract=False, cores=1, mem=11.4, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:02:53,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:02:53,079 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:02:53,096 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:02:53,116 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Working directory for job is: /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs.runners DEBUG 2024-08-30 13:02:53,127 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [59] queued (47.321 ms) +galaxy.jobs.handler INFO 2024-08-30 13:02:53,131 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:02:53,137 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 59 +galaxy.jobs DEBUG 2024-08-30 13:02:53,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [59] prepared (70.729 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:02:53,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:02:53,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:02:53,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:02:53,288 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/59/tool_script.sh] for tool command [export MPLBACKEND="agg" && poretools hist '/galaxy/server/database/objects/3/1/4/dataset_31467151-7d33-4d0c-a100-9ed18f2b85be.dat' --saveas histogram.pdf --min-length 0 --max-length 1000000000 --num-bins 50 && mv histogram.pdf '/galaxy/server/database/objects/9/1/0/dataset_910b08e1-40f5-45eb-90a8-f77f403c3c73.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:02:53,303 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (59) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/59/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/59/galaxy_59.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:02:53,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:02:53,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:02:53,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:03:00,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 59: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:03:05,668 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 59 finished +galaxy.model.metadata DEBUG 2024-08-30 13:03:05,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 74 +galaxy.util WARNING 2024-08-30 13:03:05,737 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/1/0/dataset_910b08e1-40f5-45eb-90a8-f77f403c3c73.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/1/0/dataset_910b08e1-40f5-45eb-90a8-f77f403c3c73.dat' +galaxy.jobs INFO 2024-08-30 13:03:05,767 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 59 in /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs DEBUG 2024-08-30 13:03:05,821 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 59 executed (122.375 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:03:09,527 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 60 +tpv.core.entities DEBUG 2024-08-30 13:03:09,569 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:03:09,570 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:03:09,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:03:09,595 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:03:09,617 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Working directory for job is: /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs.runners DEBUG 2024-08-30 13:03:09,626 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [60] queued (49.481 ms) +galaxy.jobs.handler INFO 2024-08-30 13:03:09,630 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:03:09,636 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 60 +galaxy.jobs DEBUG 2024-08-30 13:03:09,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [60] prepared (98.614 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:03:09,782 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/60/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/60/registry.xml' '/galaxy/server/database/jobs_directory/000/60/upload_params.json' '75:/galaxy/server/database/objects/c/e/a/dataset_cea96354-2672-45e7-a710-006d866d1524_files:/galaxy/server/database/objects/c/e/a/dataset_cea96354-2672-45e7-a710-006d866d1524.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:03:09,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (60) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/60/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/60/galaxy_60.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:03:18,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 60: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:03:24,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 60 finished +galaxy.model.metadata DEBUG 2024-08-30 13:03:24,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 75 +galaxy.jobs INFO 2024-08-30 13:03:24,149 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 60 in /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs DEBUG 2024-08-30 13:03:24,221 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 60 executed (152.945 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:03:24,984 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 61 +tpv.core.entities DEBUG 2024-08-30 13:03:25,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/.*, abstract=False, cores=1, mem=11.4, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:03:25,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:03:25,030 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:03:25,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:03:25,069 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Working directory for job is: /galaxy/server/database/jobs_directory/000/61 +galaxy.jobs.runners DEBUG 2024-08-30 13:03:25,078 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [61] queued (48.552 ms) +galaxy.jobs.handler INFO 2024-08-30 13:03:25,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:03:25,089 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 61 +galaxy.jobs DEBUG 2024-08-30 13:03:25,189 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [61] prepared (76.561 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:03:25,189 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:03:25,190 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:03:25,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:03:25,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/61/tool_script.sh] for tool command [export MPLBACKEND="agg" && poretools hist '/galaxy/server/database/objects/c/e/a/dataset_cea96354-2672-45e7-a710-006d866d1524.dat' --saveas histogram.svg --min-length 0 --max-length 1000000000 --num-bins 50 && mv histogram.svg '/galaxy/server/database/objects/8/3/6/dataset_836c00e8-a52e-41ff-9aed-169c2737422e.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:03:25,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (61) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/61/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/61/galaxy_61.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:03:25,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:03:25,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:03:25,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2024-08-30 13:03:30,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.18.96.1:443/apis/batch/v1/namespaces/prod-24-08-30-12-32-1/jobs/gxy-qbhxr + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-qbhxr": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:03:30,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (61/gxy-qbhxr) Terminated at user's request +galaxy.util WARNING 2024-08-30 13:03:30,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/8/3/6/dataset_836c00e8-a52e-41ff-9aed-169c2737422e.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/8/3/6/dataset_836c00e8-a52e-41ff-9aed-169c2737422e.dat' +galaxy.jobs.handler DEBUG 2024-08-30 13:03:34,281 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 62 +tpv.core.entities DEBUG 2024-08-30 13:03:34,318 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:03:34,319 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:03:34,323 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:03:34,341 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:03:34,359 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Working directory for job is: /galaxy/server/database/jobs_directory/000/62 +galaxy.jobs.runners DEBUG 2024-08-30 13:03:34,368 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [62] queued (44.857 ms) +galaxy.jobs.handler INFO 2024-08-30 13:03:34,373 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:03:34,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 62 +galaxy.jobs DEBUG 2024-08-30 13:03:34,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [62] prepared (111.695 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:03:34,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/62/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/62/registry.xml' '/galaxy/server/database/jobs_directory/000/62/upload_params.json' '77:/galaxy/server/database/objects/3/6/a/dataset_36ad315c-c851-4298-9586-77480d086cb7_files:/galaxy/server/database/objects/3/6/a/dataset_36ad315c-c851-4298-9586-77480d086cb7.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:03:34,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (62) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/62/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/62/galaxy_62.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-08-30 13:03:35,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 63 +tpv.core.entities DEBUG 2024-08-30 13:03:35,408 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:03:35,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:03:35,414 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:03:35,431 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:03:35,450 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Working directory for job is: /galaxy/server/database/jobs_directory/000/63 +galaxy.jobs.runners DEBUG 2024-08-30 13:03:35,457 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [63] queued (43.294 ms) +galaxy.jobs.handler INFO 2024-08-30 13:03:35,464 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:03:35,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 63 +galaxy.jobs DEBUG 2024-08-30 13:03:35,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [63] prepared (103.761 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:03:35,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/63/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/63/registry.xml' '/galaxy/server/database/jobs_directory/000/63/upload_params.json' '78:/galaxy/server/database/objects/d/0/9/dataset_d091e297-9814-44d0-81f9-bde5eff59c9a_files:/galaxy/server/database/objects/d/0/9/dataset_d091e297-9814-44d0-81f9-bde5eff59c9a.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:03:35,639 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (63) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/63/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/63/galaxy_63.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:03:43,616 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 62: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:03:44,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 63: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:03:48,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 62 finished +galaxy.model.metadata DEBUG 2024-08-30 13:03:48,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 77 +galaxy.jobs INFO 2024-08-30 13:03:48,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 62 in /galaxy/server/database/jobs_directory/000/62 +galaxy.jobs DEBUG 2024-08-30 13:03:49,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 62 executed (151.727 ms) +galaxy.jobs.runners DEBUG 2024-08-30 13:03:49,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 63 finished +galaxy.model.metadata DEBUG 2024-08-30 13:03:49,863 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 78 +galaxy.jobs INFO 2024-08-30 13:03:49,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 63 in /galaxy/server/database/jobs_directory/000/63 +galaxy.jobs DEBUG 2024-08-30 13:03:49,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 63 executed (154.239 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:03:50,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 64 +tpv.core.entities DEBUG 2024-08-30 13:03:51,044 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/.*, abstract=False, cores=10, mem=30, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:03:51,044 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:03:51,052 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:03:51,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:03:51,094 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Working directory for job is: /galaxy/server/database/jobs_directory/000/64 +galaxy.jobs.runners DEBUG 2024-08-30 13:03:51,105 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [64] queued (52.810 ms) +galaxy.jobs.handler INFO 2024-08-30 13:03:51,109 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:03:51,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 64 +galaxy.jobs DEBUG 2024-08-30 13:03:51,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [64] prepared (95.732 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:03:51,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:03:51,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:03:51,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:03:51,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/64/tool_script.sh] for tool command [computeMatrix --version > /galaxy/server/database/jobs_directory/000/64/outputs/COMMAND_VERSION 2>&1; +ln -f -s '/galaxy/server/database/objects/d/0/9/dataset_d091e297-9814-44d0-81f9-bde5eff59c9a.dat' 'bamCoverage_result4.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/3/6/a/dataset_36ad315c-c851-4298-9586-77480d086cb7.dat' 'computeMatrix1_bed_0.bed' && computeMatrix reference-point --regionsFileName 'computeMatrix1_bed_0.bed' --scoreFileName 'bamCoverage_result4.bw_0.bw' --outFileName '/galaxy/server/database/objects/9/4/d/dataset_94dca09d-bbee-4556-a511-a4b62e5e105b.dat' --samplesLabel 'bamCoverage_result4.bw' --numberOfProcessors "${GALAXY_SLOTS:-4}" --referencePoint TSS --beforeRegionStartLength 10 --afterRegionStartLength 10 --sortRegions 'keep' --sortUsing 'sum' --averageTypeBins 'sum' --binSize 10 --transcriptID transcript --exonID exon --transcript_id_designator transcript_id] +galaxy.jobs.runners DEBUG 2024-08-30 13:03:51,472 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (64) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/64/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/64/galaxy_64.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:03:51,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:03:51,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:03:51,509 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:04:18,173 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 64: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:04:23,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 64 finished +galaxy.model.metadata DEBUG 2024-08-30 13:04:23,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 79 +galaxy.util WARNING 2024-08-30 13:04:23,291 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/4/d/dataset_94dca09d-bbee-4556-a511-a4b62e5e105b.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/4/d/dataset_94dca09d-bbee-4556-a511-a4b62e5e105b.dat' +galaxy.jobs INFO 2024-08-30 13:04:23,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 64 in /galaxy/server/database/jobs_directory/000/64 +galaxy.jobs DEBUG 2024-08-30 13:04:23,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 64 executed (169.218 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:04:25,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 65 +tpv.core.entities DEBUG 2024-08-30 13:04:26,016 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:04:26,016 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:04:26,021 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:04:26,041 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:04:26,064 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Working directory for job is: /galaxy/server/database/jobs_directory/000/65 +galaxy.jobs.runners DEBUG 2024-08-30 13:04:26,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [65] queued (52.146 ms) +galaxy.jobs.handler INFO 2024-08-30 13:04:26,078 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:04:26,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 65 +galaxy.jobs DEBUG 2024-08-30 13:04:26,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [65] prepared (117.376 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:04:26,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/65/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/65/registry.xml' '/galaxy/server/database/jobs_directory/000/65/upload_params.json' '80:/galaxy/server/database/objects/c/3/d/dataset_c3de79b2-2c5b-4f58-a4ec-959fb55be1c3_files:/galaxy/server/database/objects/c/3/d/dataset_c3de79b2-2c5b-4f58-a4ec-959fb55be1c3.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:04:26,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (65) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/65/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/65/galaxy_65.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-08-30 13:04:27,080 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 66 +tpv.core.entities DEBUG 2024-08-30 13:04:27,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:04:27,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:04:27,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:04:27,141 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:04:27,164 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Working directory for job is: /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs.runners DEBUG 2024-08-30 13:04:27,174 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [66] queued (50.004 ms) +galaxy.jobs.handler INFO 2024-08-30 13:04:27,179 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:04:27,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 66 +galaxy.jobs DEBUG 2024-08-30 13:04:27,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [66] prepared (103.872 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:04:27,338 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/66/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/66/registry.xml' '/galaxy/server/database/jobs_directory/000/66/upload_params.json' '81:/galaxy/server/database/objects/9/b/1/dataset_9b1ab5f4-4dca-43fe-a030-f321a3fdf0e4_files:/galaxy/server/database/objects/9/b/1/dataset_9b1ab5f4-4dca-43fe-a030-f321a3fdf0e4.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:04:27,352 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (66) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/66/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/66/galaxy_66.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:04:34,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 65: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:04:36,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 66: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:04:40,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 65 finished +galaxy.model.metadata DEBUG 2024-08-30 13:04:40,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 80 +galaxy.jobs INFO 2024-08-30 13:04:40,137 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 65 in /galaxy/server/database/jobs_directory/000/65 +galaxy.jobs DEBUG 2024-08-30 13:04:40,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 65 executed (135.245 ms) +galaxy.jobs.runners DEBUG 2024-08-30 13:04:41,017 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 66 finished +galaxy.model.metadata DEBUG 2024-08-30 13:04:41,091 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 81 +galaxy.jobs INFO 2024-08-30 13:04:41,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 66 in /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs DEBUG 2024-08-30 13:04:41,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 66 executed (163.013 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:04:42,541 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 67 +tpv.core.entities DEBUG 2024-08-30 13:04:42,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/.*, abstract=False, cores=10, mem=30, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:04:42,588 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:04:42,597 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:04:42,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:04:42,640 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Working directory for job is: /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs.runners DEBUG 2024-08-30 13:04:42,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [67] queued (51.986 ms) +galaxy.jobs.handler INFO 2024-08-30 13:04:42,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:04:42,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 67 +galaxy.jobs DEBUG 2024-08-30 13:04:42,759 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [67] prepared (78.223 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:04:42,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:04:42,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:04:42,783 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:04:42,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/67/tool_script.sh] for tool command [computeMatrix --version > /galaxy/server/database/jobs_directory/000/67/outputs/COMMAND_VERSION 2>&1; +ln -f -s '/galaxy/server/database/objects/9/b/1/dataset_9b1ab5f4-4dca-43fe-a030-f321a3fdf0e4.dat' 'computeMatrix2.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/c/3/d/dataset_c3de79b2-2c5b-4f58-a4ec-959fb55be1c3.dat' 'computeMatrix2_bed_0.bed' && computeMatrix reference-point --regionsFileName 'computeMatrix2_bed_0.bed' --scoreFileName 'computeMatrix2.bw_0.bw' --outFileName '/galaxy/server/database/objects/b/c/b/dataset_bcb97d3c-b445-46b8-bd04-19e1e086f8a7.dat' --samplesLabel 'computeMatrix2.bw' --numberOfProcessors "${GALAXY_SLOTS:-4}" --referencePoint TSS --beforeRegionStartLength 10 --afterRegionStartLength 10 --sortRegions 'keep' --sortUsing 'mean' --averageTypeBins 'mean' --binSize 10 --transcriptID transcript --exonID exon --transcript_id_designator transcript_id] +galaxy.jobs.runners DEBUG 2024-08-30 13:04:42,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (67) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/67/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/67/galaxy_67.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:04:42,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:04:42,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:04:42,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:04:49,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 67: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:04:54,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 67 finished +galaxy.model.metadata DEBUG 2024-08-30 13:04:54,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 82 +galaxy.util WARNING 2024-08-30 13:04:54,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/b/c/b/dataset_bcb97d3c-b445-46b8-bd04-19e1e086f8a7.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/b/c/b/dataset_bcb97d3c-b445-46b8-bd04-19e1e086f8a7.dat' +galaxy.jobs INFO 2024-08-30 13:04:54,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 67 in /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs DEBUG 2024-08-30 13:04:54,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 67 executed (143.255 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:04:56,989 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 68 +tpv.core.entities DEBUG 2024-08-30 13:04:57,028 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:04:57,029 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:04:57,035 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:04:57,055 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:04:57,077 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Working directory for job is: /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs.runners DEBUG 2024-08-30 13:04:57,086 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [68] queued (50.822 ms) +galaxy.jobs.handler INFO 2024-08-30 13:04:57,090 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:04:57,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 68 +galaxy.jobs DEBUG 2024-08-30 13:04:57,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [68] prepared (110.052 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:04:57,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/68/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/68/registry.xml' '/galaxy/server/database/jobs_directory/000/68/upload_params.json' '83:/galaxy/server/database/objects/a/3/1/dataset_a3100f19-1c62-4980-9777-88d9c603ea51_files:/galaxy/server/database/objects/a/3/1/dataset_a3100f19-1c62-4980-9777-88d9c603ea51.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:04:57,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (68) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/68/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/68/galaxy_68.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-08-30 13:04:58,093 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 69 +tpv.core.entities DEBUG 2024-08-30 13:04:58,129 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:04:58,129 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:04:58,135 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:04:58,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:04:58,177 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Working directory for job is: /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs.runners DEBUG 2024-08-30 13:04:58,186 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [69] queued (50.142 ms) +galaxy.jobs.handler INFO 2024-08-30 13:04:58,190 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:04:58,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 69 +galaxy.jobs DEBUG 2024-08-30 13:04:58,335 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [69] prepared (113.978 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:04:58,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/69/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/69/registry.xml' '/galaxy/server/database/jobs_directory/000/69/upload_params.json' '84:/galaxy/server/database/objects/4/c/4/dataset_4c462518-cffb-40de-beef-22f00860aec2_files:/galaxy/server/database/objects/4/c/4/dataset_4c462518-cffb-40de-beef-22f00860aec2.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:04:58,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (69) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/69/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/69/galaxy_69.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:05:05,453 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 68: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:05:06,652 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 69: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:05:10,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 68 finished +galaxy.model.metadata DEBUG 2024-08-30 13:05:10,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 83 +galaxy.jobs INFO 2024-08-30 13:05:10,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 68 in /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs DEBUG 2024-08-30 13:05:11,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 68 executed (167.389 ms) +galaxy.jobs.runners DEBUG 2024-08-30 13:05:11,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 69 finished +galaxy.model.metadata DEBUG 2024-08-30 13:05:11,944 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 84 +galaxy.jobs INFO 2024-08-30 13:05:11,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 69 in /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs DEBUG 2024-08-30 13:05:12,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 69 executed (164.267 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:05:12,883 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 70 +tpv.core.entities DEBUG 2024-08-30 13:05:12,938 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/.*, abstract=False, cores=10, mem=30, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:05:12,938 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:05:12,946 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:05:12,969 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:05:12,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Working directory for job is: /galaxy/server/database/jobs_directory/000/70 +galaxy.jobs.runners DEBUG 2024-08-30 13:05:13,006 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [70] queued (59.313 ms) +galaxy.jobs.handler INFO 2024-08-30 13:05:13,010 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:05:13,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 70 +galaxy.jobs DEBUG 2024-08-30 13:05:13,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [70] prepared (84.498 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:05:13,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:05:13,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:05:13,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:05:13,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/70/tool_script.sh] for tool command [computeMatrix --version > /galaxy/server/database/jobs_directory/000/70/outputs/COMMAND_VERSION 2>&1; +ln -f -s '/galaxy/server/database/objects/4/c/4/dataset_4c462518-cffb-40de-beef-22f00860aec2.dat' 'computeMatrix2.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/a/3/1/dataset_a3100f19-1c62-4980-9777-88d9c603ea51.dat' 'computeMatrix2_bed_0.bed' && computeMatrix scale-regions --regionsFileName 'computeMatrix2_bed_0.bed' --scoreFileName 'computeMatrix2.bw_0.bw' --outFileName '/galaxy/server/database/objects/f/5/d/dataset_f5d34cd0-fd0d-4cc8-b1e6-af2386f4a891.dat' --samplesLabel 'computeMatrix2.bw' --numberOfProcessors "${GALAXY_SLOTS:-4}" --regionBodyLength 500 --sortRegions 'keep' --sortUsing 'mean' --averageTypeBins 'mean' --binSize 50 --transcriptID transcript --exonID exon --transcript_id_designator transcript_id] +galaxy.jobs.runners DEBUG 2024-08-30 13:05:13,390 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (70) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/70/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/70/galaxy_70.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:05:13,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:05:13,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:05:13,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:05:18,637 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 70: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:05:23,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 70 finished +galaxy.model.metadata DEBUG 2024-08-30 13:05:23,896 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 85 +galaxy.util WARNING 2024-08-30 13:05:23,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/5/d/dataset_f5d34cd0-fd0d-4cc8-b1e6-af2386f4a891.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/5/d/dataset_f5d34cd0-fd0d-4cc8-b1e6-af2386f4a891.dat' +galaxy.jobs INFO 2024-08-30 13:05:23,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 70 in /galaxy/server/database/jobs_directory/000/70 +galaxy.jobs DEBUG 2024-08-30 13:05:24,001 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 70 executed (152.827 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:05:28,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 71 +tpv.core.entities DEBUG 2024-08-30 13:05:28,422 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:05:28,423 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:05:28,429 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:05:28,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:05:28,471 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Working directory for job is: /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs.runners DEBUG 2024-08-30 13:05:28,479 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [71] queued (49.914 ms) +galaxy.jobs.handler INFO 2024-08-30 13:05:28,483 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:05:28,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 71 +galaxy.jobs DEBUG 2024-08-30 13:05:28,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [71] prepared (109.420 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:05:28,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/71/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/71/registry.xml' '/galaxy/server/database/jobs_directory/000/71/upload_params.json' '86:/galaxy/server/database/objects/2/4/1/dataset_24199aa4-d69a-4199-8d54-5aec551c087d_files:/galaxy/server/database/objects/2/4/1/dataset_24199aa4-d69a-4199-8d54-5aec551c087d.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:05:28,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (71) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/71/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/71/galaxy_71.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:05:37,860 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 71: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:05:42,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 71 finished +galaxy.model.metadata DEBUG 2024-08-30 13:05:42,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 86 +galaxy.jobs INFO 2024-08-30 13:05:42,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 71 in /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs DEBUG 2024-08-30 13:05:43,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 71 executed (183.817 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:05:43,858 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 72 +tpv.core.entities DEBUG 2024-08-30 13:05:43,904 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/.*, abstract=False, cores=10, mem=24, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:05:43,905 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:05:43,910 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:05:43,928 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:05:43,950 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Working directory for job is: /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs.runners DEBUG 2024-08-30 13:05:43,959 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [72] queued (48.349 ms) +galaxy.jobs.handler INFO 2024-08-30 13:05:43,963 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:05:43,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 72 +galaxy.jobs DEBUG 2024-08-30 13:05:44,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [72] prepared (86.080 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:05:44,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:05:44,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:05:44,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:05:44,128 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/72/tool_script.sh] for tool command [bamCoverage --version > /galaxy/server/database/jobs_directory/000/72/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/2/4/1/dataset_24199aa4-d69a-4199-8d54-5aec551c087d.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/3/6/8/metadata_3688c290-7b37-43e5-af69-fbdff8bae1ad.dat' one.bam.bai && bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}" --bam one.bam --outFileName '/galaxy/server/database/objects/1/6/7/dataset_167b4e7b-54b1-4fbd-9556-c163ab456185.dat' --outFileFormat 'bigwig' --binSize 10] +galaxy.jobs.runners DEBUG 2024-08-30 13:05:44,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (72) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/72/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/72/galaxy_72.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:05:44,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:05:44,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:05:44,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:05:48,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 72: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:05:54,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 72 finished +galaxy.model.metadata DEBUG 2024-08-30 13:05:54,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 87 +galaxy.util WARNING 2024-08-30 13:05:54,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/1/6/7/dataset_167b4e7b-54b1-4fbd-9556-c163ab456185.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/1/6/7/dataset_167b4e7b-54b1-4fbd-9556-c163ab456185.dat' +galaxy.jobs INFO 2024-08-30 13:05:54,197 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 72 in /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs DEBUG 2024-08-30 13:05:54,272 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 72 executed (169.821 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:05:57,271 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 73 +tpv.core.entities DEBUG 2024-08-30 13:05:57,307 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:05:57,307 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:05:57,313 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:05:57,329 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:05:57,348 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Working directory for job is: /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs.runners DEBUG 2024-08-30 13:05:57,355 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [73] queued (42.578 ms) +galaxy.jobs.handler INFO 2024-08-30 13:05:57,359 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:05:57,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 73 +galaxy.jobs DEBUG 2024-08-30 13:05:57,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [73] prepared (101.118 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:05:57,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/73/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/73/registry.xml' '/galaxy/server/database/jobs_directory/000/73/upload_params.json' '88:/galaxy/server/database/objects/6/2/2/dataset_62204f6e-8047-45b5-a698-b68e50bac7d5_files:/galaxy/server/database/objects/6/2/2/dataset_62204f6e-8047-45b5-a698-b68e50bac7d5.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:05:57,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (73) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/73/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/73/galaxy_73.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:06:07,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 73: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:06:12,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 73 finished +galaxy.model.metadata DEBUG 2024-08-30 13:06:12,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 88 +galaxy.jobs INFO 2024-08-30 13:06:12,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 73 in /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs DEBUG 2024-08-30 13:06:12,468 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 73 executed (186.232 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:06:13,697 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 74 +tpv.core.entities DEBUG 2024-08-30 13:06:13,735 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/.*, abstract=False, cores=10, mem=24, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:06:13,735 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:06:13,740 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:06:13,753 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:06:13,770 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Working directory for job is: /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs.runners DEBUG 2024-08-30 13:06:13,778 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [74] queued (37.807 ms) +galaxy.jobs.handler INFO 2024-08-30 13:06:13,781 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:06:13,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 74 +galaxy.jobs DEBUG 2024-08-30 13:06:13,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [74] prepared (76.378 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:06:13,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:06:13,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:06:13,908 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:06:13,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/74/tool_script.sh] for tool command [bamCoverage --version > /galaxy/server/database/jobs_directory/000/74/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/6/2/2/dataset_62204f6e-8047-45b5-a698-b68e50bac7d5.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/b/2/b/metadata_b2b49118-b465-417d-b858-f1f54d33a292.dat' one.bam.bai && bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}" --bam one.bam --outFileName '/galaxy/server/database/objects/4/6/0/dataset_4609bcf0-2af2-46c7-b164-a2589c3c4fae.dat' --outFileFormat 'bigwig' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000] +galaxy.jobs.runners DEBUG 2024-08-30 13:06:13,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (74) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/74/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/74/galaxy_74.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:06:13,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:06:13,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:06:13,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:06:19,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 74: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:06:24,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 74 finished +galaxy.model.metadata DEBUG 2024-08-30 13:06:24,779 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 89 +galaxy.util WARNING 2024-08-30 13:06:24,787 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/6/0/dataset_4609bcf0-2af2-46c7-b164-a2589c3c4fae.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/6/0/dataset_4609bcf0-2af2-46c7-b164-a2589c3c4fae.dat' +galaxy.jobs INFO 2024-08-30 13:06:24,826 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 74 in /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs DEBUG 2024-08-30 13:06:24,896 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 74 executed (160.197 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:06:28,122 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 75 +tpv.core.entities DEBUG 2024-08-30 13:06:28,164 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:06:28,164 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:06:28,169 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:06:28,185 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:06:28,205 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Working directory for job is: /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs.runners DEBUG 2024-08-30 13:06:28,213 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [75] queued (43.512 ms) +galaxy.jobs.handler INFO 2024-08-30 13:06:28,218 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:06:28,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 75 +galaxy.jobs DEBUG 2024-08-30 13:06:28,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [75] prepared (100.888 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:06:28,368 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/75/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/75/registry.xml' '/galaxy/server/database/jobs_directory/000/75/upload_params.json' '90:/galaxy/server/database/objects/d/f/f/dataset_dffaa440-2d02-4392-8f8e-421ef7cbe075_files:/galaxy/server/database/objects/d/f/f/dataset_dffaa440-2d02-4392-8f8e-421ef7cbe075.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:06:28,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (75) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/75/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/75/galaxy_75.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:06:36,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 75: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:06:41,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 75 finished +galaxy.model.metadata DEBUG 2024-08-30 13:06:41,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 90 +galaxy.jobs INFO 2024-08-30 13:06:41,782 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 75 in /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs DEBUG 2024-08-30 13:06:41,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 75 executed (198.073 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:06:42,545 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 76 +tpv.core.entities DEBUG 2024-08-30 13:06:42,586 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/.*, abstract=False, cores=10, mem=24, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:06:42,586 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:06:42,593 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:06:42,615 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:06:42,639 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Working directory for job is: /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs.runners DEBUG 2024-08-30 13:06:42,648 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [76] queued (55.541 ms) +galaxy.jobs.handler INFO 2024-08-30 13:06:42,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:06:42,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 76 +galaxy.jobs DEBUG 2024-08-30 13:06:42,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [76] prepared (65.953 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:06:42,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:06:42,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:06:42,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:06:42,795 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/76/tool_script.sh] for tool command [bamCoverage --version > /galaxy/server/database/jobs_directory/000/76/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/d/f/f/dataset_dffaa440-2d02-4392-8f8e-421ef7cbe075.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/7/1/4/metadata_7146906b-6599-4fa2-b478-68f7f2c8e756.dat' one.bam.bai && bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}" --bam one.bam --outFileName '/galaxy/server/database/objects/a/7/d/dataset_a7dc6700-a27c-4922-bf0e-c82c8a97e23c.dat' --outFileFormat 'bedgraph' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000] +galaxy.jobs.runners DEBUG 2024-08-30 13:06:42,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (76) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/76/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/76/galaxy_76.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:06:42,822 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:06:42,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:06:42,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:06:48,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 76: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:06:52,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 76 finished +galaxy.model.metadata DEBUG 2024-08-30 13:06:52,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 91 +galaxy.util WARNING 2024-08-30 13:06:53,007 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/a/7/d/dataset_a7dc6700-a27c-4922-bf0e-c82c8a97e23c.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/7/d/dataset_a7dc6700-a27c-4922-bf0e-c82c8a97e23c.dat' +galaxy.jobs INFO 2024-08-30 13:06:53,041 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 76 in /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs DEBUG 2024-08-30 13:06:53,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 76 executed (158.684 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:06:55,950 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 77 +tpv.core.entities DEBUG 2024-08-30 13:06:55,989 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:06:55,990 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:06:55,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:06:56,012 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:06:56,034 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Working directory for job is: /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs.runners DEBUG 2024-08-30 13:06:56,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [77] queued (47.506 ms) +galaxy.jobs.handler INFO 2024-08-30 13:06:56,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:06:56,053 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 77 +galaxy.jobs DEBUG 2024-08-30 13:06:56,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [77] prepared (115.842 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:06:56,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/77/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/77/registry.xml' '/galaxy/server/database/jobs_directory/000/77/upload_params.json' '92:/galaxy/server/database/objects/5/8/c/dataset_58c8ab4c-194d-40f6-8a4e-e1521e586719_files:/galaxy/server/database/objects/5/8/c/dataset_58c8ab4c-194d-40f6-8a4e-e1521e586719.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:06:56,243 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (77) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/77/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/77/galaxy_77.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:07:05,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 77: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:07:10,477 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 77 finished +galaxy.model.metadata DEBUG 2024-08-30 13:07:10,545 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 92 +galaxy.jobs INFO 2024-08-30 13:07:10,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 77 in /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs DEBUG 2024-08-30 13:07:10,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 77 executed (191.235 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:07:11,588 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 78 +tpv.core.entities DEBUG 2024-08-30 13:07:11,635 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/.*, abstract=False, cores=10, mem=24, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:07:11,635 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:07:11,643 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:07:11,663 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:07:11,688 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Working directory for job is: /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs.runners DEBUG 2024-08-30 13:07:11,698 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [78] queued (55.214 ms) +galaxy.jobs.handler INFO 2024-08-30 13:07:11,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:07:11,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 78 +galaxy.jobs DEBUG 2024-08-30 13:07:11,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [78] prepared (71.647 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:07:11,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:07:11,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:07:11,828 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:07:11,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/78/tool_script.sh] for tool command [bamCoverage --version > /galaxy/server/database/jobs_directory/000/78/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/5/8/c/dataset_58c8ab4c-194d-40f6-8a4e-e1521e586719.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/2/c/3/metadata_2c358893-1e49-4d64-bc55-c4cccab338d5.dat' one.bam.bai && bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}" --bam one.bam --outFileName '/galaxy/server/database/objects/f/0/6/dataset_f060a4c7-ff5a-4892-b273-51e1ee4e153a.dat' --outFileFormat 'bigwig' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000] +galaxy.jobs.runners DEBUG 2024-08-30 13:07:11,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (78) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/78/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/78/galaxy_78.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:07:11,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:07:11,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:07:11,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:07:17,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 78: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:07:22,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 78 finished +galaxy.model.metadata DEBUG 2024-08-30 13:07:22,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 93 +galaxy.util WARNING 2024-08-30 13:07:22,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/0/6/dataset_f060a4c7-ff5a-4892-b273-51e1ee4e153a.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/0/6/dataset_f060a4c7-ff5a-4892-b273-51e1ee4e153a.dat' +galaxy.jobs INFO 2024-08-30 13:07:22,502 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 78 in /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs DEBUG 2024-08-30 13:07:22,569 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 78 executed (153.891 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:07:25,003 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 79 +tpv.core.entities DEBUG 2024-08-30 13:07:25,042 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:07:25,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:07:25,048 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:07:25,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:07:25,093 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Working directory for job is: /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs.runners DEBUG 2024-08-30 13:07:25,102 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [79] queued (52.918 ms) +galaxy.jobs.handler INFO 2024-08-30 13:07:25,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:07:25,111 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 79 +galaxy.jobs DEBUG 2024-08-30 13:07:25,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [79] prepared (124.243 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:07:25,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/79/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/79/registry.xml' '/galaxy/server/database/jobs_directory/000/79/upload_params.json' '94:/galaxy/server/database/objects/5/4/b/dataset_54b0d192-c778-471c-8242-7d1c2e3170a1_files:/galaxy/server/database/objects/5/4/b/dataset_54b0d192-c778-471c-8242-7d1c2e3170a1.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:07:25,301 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (79) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/79/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/79/galaxy_79.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:07:33,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 79: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:07:38,785 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 79 finished +galaxy.model.metadata DEBUG 2024-08-30 13:07:38,857 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 94 +galaxy.jobs INFO 2024-08-30 13:07:38,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 79 in /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs DEBUG 2024-08-30 13:07:39,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 79 executed (201.694 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:07:39,450 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 80 +tpv.core.entities DEBUG 2024-08-30 13:07:39,498 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/.*, abstract=False, cores=10, mem=24, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:07:39,498 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:07:39,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:07:39,526 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:07:39,549 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Working directory for job is: /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs.runners DEBUG 2024-08-30 13:07:39,558 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [80] queued (51.822 ms) +galaxy.jobs.handler INFO 2024-08-30 13:07:39,562 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:07:39,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 80 +galaxy.jobs DEBUG 2024-08-30 13:07:39,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [80] prepared (71.112 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:07:39,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:07:39,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:07:39,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:07:39,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/80/tool_script.sh] for tool command [bamCoverage --version > /galaxy/server/database/jobs_directory/000/80/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/5/4/b/dataset_54b0d192-c778-471c-8242-7d1c2e3170a1.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/f/c/f/metadata_fcf7221d-eef9-45a6-a569-74221ec4cd00.dat' one.bam.bai && bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}" --bam one.bam --outFileName '/galaxy/server/database/objects/8/4/3/dataset_843bde66-95bb-404e-8b4c-42447c462c0b.dat' --outFileFormat 'bedgraph' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000 --scaleFactor 1.0 --minMappingQuality '1'] +galaxy.jobs.runners DEBUG 2024-08-30 13:07:39,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (80) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/80/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/80/galaxy_80.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:07:39,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:07:39,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:07:39,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:07:44,944 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 80: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:07:49,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 80 finished +galaxy.model.metadata DEBUG 2024-08-30 13:07:49,871 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 95 +galaxy.util WARNING 2024-08-30 13:07:49,881 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/8/4/3/dataset_843bde66-95bb-404e-8b4c-42447c462c0b.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/8/4/3/dataset_843bde66-95bb-404e-8b4c-42447c462c0b.dat' +galaxy.jobs INFO 2024-08-30 13:07:49,914 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 80 in /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs DEBUG 2024-08-30 13:07:49,970 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 80 executed (137.912 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:07:52,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 81 +tpv.core.entities DEBUG 2024-08-30 13:07:52,908 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:07:52,908 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:07:52,915 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:07:52,932 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:07:52,954 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Working directory for job is: /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs.runners DEBUG 2024-08-30 13:07:52,963 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [81] queued (47.741 ms) +galaxy.jobs.handler INFO 2024-08-30 13:07:52,967 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:07:52,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 81 +galaxy.jobs DEBUG 2024-08-30 13:07:53,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [81] prepared (103.952 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:07:53,128 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/81/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/81/registry.xml' '/galaxy/server/database/jobs_directory/000/81/upload_params.json' '96:/galaxy/server/database/objects/b/b/4/dataset_bb442541-d924-4bf9-9e47-2d1fb0c0be91_files:/galaxy/server/database/objects/b/b/4/dataset_bb442541-d924-4bf9-9e47-2d1fb0c0be91.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:07:53,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (81) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/81/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/81/galaxy_81.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:08:02,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 81: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:08:07,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 81 finished +galaxy.model.metadata DEBUG 2024-08-30 13:08:07,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 96 +galaxy.jobs INFO 2024-08-30 13:08:07,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 81 in /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs DEBUG 2024-08-30 13:08:07,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 81 executed (196.451 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:08:08,392 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 82 +tpv.core.entities DEBUG 2024-08-30 13:08:08,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/.*, abstract=False, cores=10, mem=24, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:08:08,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:08:08,441 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:08:08,457 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:08:08,478 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Working directory for job is: /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs.runners DEBUG 2024-08-30 13:08:08,489 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [82] queued (48.418 ms) +galaxy.jobs.handler INFO 2024-08-30 13:08:08,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:08:08,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 82 +galaxy.jobs DEBUG 2024-08-30 13:08:08,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [82] prepared (78.922 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:08:08,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:08:08,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:08:08,625 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:08:08,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/82/tool_script.sh] for tool command [bamCoverage --version > /galaxy/server/database/jobs_directory/000/82/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/b/b/4/dataset_bb442541-d924-4bf9-9e47-2d1fb0c0be91.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/c/3/c/metadata_c3c939e3-98d0-4521-bada-4827a472be86.dat' one.bam.bai && bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}" --bam one.bam --outFileName '/galaxy/server/database/objects/0/2/a/dataset_02a269e2-737e-4759-9f4f-b13347209855.dat' --outFileFormat 'bigwig' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000 --scaleFactor 1.0 --minMappingQuality '1' --filterRNAstrand 'reverse'] +galaxy.jobs.runners DEBUG 2024-08-30 13:08:08,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (82) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/82/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/82/galaxy_82.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:08:08,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:08:08,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:08:08,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:08:13,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 82: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:08:18,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 82 finished +galaxy.model.metadata DEBUG 2024-08-30 13:08:18,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 97 +galaxy.util WARNING 2024-08-30 13:08:18,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/0/2/a/dataset_02a269e2-737e-4759-9f4f-b13347209855.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/0/2/a/dataset_02a269e2-737e-4759-9f4f-b13347209855.dat' +galaxy.jobs INFO 2024-08-30 13:08:18,487 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 82 in /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs DEBUG 2024-08-30 13:08:18,544 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 82 executed (132.056 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:08:21,801 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 83 +tpv.core.entities DEBUG 2024-08-30 13:08:21,840 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:08:21,841 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:08:21,847 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:08:21,867 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:08:21,889 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Working directory for job is: /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs.runners DEBUG 2024-08-30 13:08:21,898 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [83] queued (50.284 ms) +galaxy.jobs.handler INFO 2024-08-30 13:08:21,902 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:08:21,907 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 83 +galaxy.jobs DEBUG 2024-08-30 13:08:22,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [83] prepared (102.818 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:08:22,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/83/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/83/registry.xml' '/galaxy/server/database/jobs_directory/000/83/upload_params.json' '98:/galaxy/server/database/objects/a/2/6/dataset_a2663303-53a7-4851-8ea3-85c2e9c3e5a2_files:/galaxy/server/database/objects/a/2/6/dataset_a2663303-53a7-4851-8ea3-85c2e9c3e5a2.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:08:22,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (83) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/83/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/83/galaxy_83.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:08:30,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 83: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:08:35,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 83 finished +galaxy.model.metadata DEBUG 2024-08-30 13:08:35,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 98 +galaxy.jobs INFO 2024-08-30 13:08:35,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 83 in /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs DEBUG 2024-08-30 13:08:36,003 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 83 executed (192.299 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:08:37,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 84 +tpv.core.entities DEBUG 2024-08-30 13:08:37,302 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/.*, abstract=False, cores=10, mem=24, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:08:37,302 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:08:37,309 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:08:37,328 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:08:37,349 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Working directory for job is: /galaxy/server/database/jobs_directory/000/84 +galaxy.jobs.runners DEBUG 2024-08-30 13:08:37,357 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [84] queued (47.328 ms) +galaxy.jobs.handler INFO 2024-08-30 13:08:37,360 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:08:37,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 84 +galaxy.jobs DEBUG 2024-08-30 13:08:37,460 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [84] prepared (70.646 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:08:37,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:08:37,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:08:37,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:08:37,510 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/84/tool_script.sh] for tool command [bamCoverage --version > /galaxy/server/database/jobs_directory/000/84/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/a/2/6/dataset_a2663303-53a7-4851-8ea3-85c2e9c3e5a2.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/6/7/6/metadata_6767c2d4-35a1-4807-840b-9daba8b6e916.dat' one.bam.bai && bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}" --bam one.bam --outFileName '/galaxy/server/database/objects/5/a/9/dataset_5a97ade3-b438-47da-bbcf-c0c0547642ed.dat' --outFileFormat 'bigwig' --binSize 10 --scaleFactor 1.0 --extendReads --Offset -4 -1] +galaxy.jobs.runners DEBUG 2024-08-30 13:08:37,524 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (84) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/84/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/84/galaxy_84.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:08:37,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:08:37,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:08:37,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:08:42,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 84: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:08:47,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 84 finished +galaxy.model.metadata DEBUG 2024-08-30 13:08:47,832 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 99 +galaxy.util WARNING 2024-08-30 13:08:47,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/a/9/dataset_5a97ade3-b438-47da-bbcf-c0c0547642ed.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/a/9/dataset_5a97ade3-b438-47da-bbcf-c0c0547642ed.dat' +galaxy.jobs INFO 2024-08-30 13:08:47,872 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 84 in /galaxy/server/database/jobs_directory/000/84 +galaxy.jobs DEBUG 2024-08-30 13:08:47,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 84 executed (144.235 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:08:52,718 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 85 +tpv.core.entities DEBUG 2024-08-30 13:08:52,760 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:08:52,761 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:08:52,767 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:08:52,786 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:08:52,809 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Working directory for job is: /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs.runners DEBUG 2024-08-30 13:08:52,817 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [85] queued (49.978 ms) +galaxy.jobs.handler INFO 2024-08-30 13:08:52,821 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:08:52,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 85 +galaxy.jobs DEBUG 2024-08-30 13:08:52,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [85] prepared (105.031 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:08:52,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/85/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/85/registry.xml' '/galaxy/server/database/jobs_directory/000/85/upload_params.json' '100:/galaxy/server/database/objects/d/3/7/dataset_d37def15-5a08-4f52-acce-7e74389bb375_files:/galaxy/server/database/objects/d/3/7/dataset_d37def15-5a08-4f52-acce-7e74389bb375.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:08:52,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (85) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/85/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/85/galaxy_85.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:09:01,949 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 85: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:09:07,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 85 finished +galaxy.model.metadata DEBUG 2024-08-30 13:09:07,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 100 +galaxy.jobs INFO 2024-08-30 13:09:07,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 85 in /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs DEBUG 2024-08-30 13:09:07,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 85 executed (215.923 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:09:08,207 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 86 +tpv.core.entities DEBUG 2024-08-30 13:09:08,249 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/.*, abstract=False, cores=1, mem=11.4, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:09:08,250 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:09:08,255 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:09:08,273 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:09:08,292 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Working directory for job is: /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs.runners DEBUG 2024-08-30 13:09:08,300 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [86] queued (44.766 ms) +galaxy.jobs.handler INFO 2024-08-30 13:09:08,305 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:09:08,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 86 +galaxy.jobs DEBUG 2024-08-30 13:09:08,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [86] prepared (67.972 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:09:08,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:09:08,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:09:08,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:09:08,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/86/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/86/outputs/COMMAND_VERSION 2>&1; +lofreq indelqual --uniform 20,30 -o output.bam /galaxy/server/database/objects/d/3/7/dataset_d37def15-5a08-4f52-acce-7e74389bb375.dat] +galaxy.jobs.runners DEBUG 2024-08-30 13:09:08,642 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (86) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/86/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/86/galaxy_86.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/86/working/output.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/86/working/output.bam" "/galaxy/server/database/objects/5/3/3/dataset_53373daf-3405-4d26-a409-3ced0d6ca9b0.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:09:08,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:09:08,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:09:08,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:09:19,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 86: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:09:24,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 86 finished +galaxy.model.metadata DEBUG 2024-08-30 13:09:24,471 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 101 +galaxy.util WARNING 2024-08-30 13:09:24,524 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/3/3/dataset_53373daf-3405-4d26-a409-3ced0d6ca9b0.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/3/3/dataset_53373daf-3405-4d26-a409-3ced0d6ca9b0.dat' +galaxy.jobs INFO 2024-08-30 13:09:24,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 86 in /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs DEBUG 2024-08-30 13:09:24,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 86 executed (191.409 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:09:27,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 87 +tpv.core.entities DEBUG 2024-08-30 13:09:27,802 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:09:27,803 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:09:27,807 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:09:27,822 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:09:27,842 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Working directory for job is: /galaxy/server/database/jobs_directory/000/87 +galaxy.jobs.runners DEBUG 2024-08-30 13:09:27,850 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [87] queued (43.353 ms) +galaxy.jobs.handler INFO 2024-08-30 13:09:27,854 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:09:27,858 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 87 +galaxy.jobs DEBUG 2024-08-30 13:09:27,984 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [87] prepared (104.831 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:09:28,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/87/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/87/registry.xml' '/galaxy/server/database/jobs_directory/000/87/upload_params.json' '102:/galaxy/server/database/objects/d/5/5/dataset_d55d6a7e-3840-4d50-bd60-5c59e885f84c_files:/galaxy/server/database/objects/d/5/5/dataset_d55d6a7e-3840-4d50-bd60-5c59e885f84c.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:09:28,031 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (87) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/87/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/87/galaxy_87.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-08-30 13:09:28,857 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 88 +tpv.core.entities DEBUG 2024-08-30 13:09:28,897 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:09:28,898 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:09:28,904 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:09:28,923 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:09:28,943 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Working directory for job is: /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs.runners DEBUG 2024-08-30 13:09:28,951 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [88] queued (47.127 ms) +galaxy.jobs.handler INFO 2024-08-30 13:09:28,955 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:09:28,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 88 +galaxy.jobs DEBUG 2024-08-30 13:09:29,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [88] prepared (111.784 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:09:29,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/88/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/88/registry.xml' '/galaxy/server/database/jobs_directory/000/88/upload_params.json' '103:/galaxy/server/database/objects/6/5/e/dataset_65e87b57-8d6e-429c-a56f-a894d04b1466_files:/galaxy/server/database/objects/6/5/e/dataset_65e87b57-8d6e-429c-a56f-a894d04b1466.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:09:29,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (88) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/88/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/88/galaxy_88.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:09:37,625 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 87: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:09:37,648 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 88: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:09:42,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 88 finished +galaxy.model.metadata DEBUG 2024-08-30 13:09:42,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 103 +galaxy.jobs INFO 2024-08-30 13:09:42,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 88 in /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs.runners DEBUG 2024-08-30 13:09:42,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 87 finished +galaxy.jobs DEBUG 2024-08-30 13:09:43,054 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 88 executed (151.823 ms) +galaxy.model.metadata DEBUG 2024-08-30 13:09:43,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 102 +galaxy.jobs INFO 2024-08-30 13:09:43,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 87 in /galaxy/server/database/jobs_directory/000/87 +galaxy.jobs DEBUG 2024-08-30 13:09:43,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 87 executed (210.024 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:09:44,326 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 89 +tpv.core.entities DEBUG 2024-08-30 13:09:44,373 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/.*, abstract=False, cores=1, mem=11.4, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:09:44,374 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:09:44,380 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:09:44,400 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:09:44,423 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Working directory for job is: /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs.runners DEBUG 2024-08-30 13:09:44,432 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [89] queued (51.074 ms) +galaxy.jobs.handler INFO 2024-08-30 13:09:44,436 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:09:44,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 89 +galaxy.jobs DEBUG 2024-08-30 13:09:44,529 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [89] prepared (68.896 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:09:44,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:09:44,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:09:44,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:09:44,586 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/89/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/89/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/6/5/e/dataset_65e87b57-8d6e-429c-a56f-a894d04b1466.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && lofreq indelqual --dindel --ref reference.fa -o output.bam /galaxy/server/database/objects/d/5/5/dataset_d55d6a7e-3840-4d50-bd60-5c59e885f84c.dat] +galaxy.jobs.runners DEBUG 2024-08-30 13:09:44,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (89) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/89/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/89/galaxy_89.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/89/working/output.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/89/working/output.bam" "/galaxy/server/database/objects/5/e/d/dataset_5edcb442-8f71-48fc-bf93-9638eee48f40.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:09:44,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:09:44,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:09:44,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:09:48,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 89: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:09:53,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 89 finished +galaxy.model.metadata DEBUG 2024-08-30 13:09:54,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 104 +galaxy.util WARNING 2024-08-30 13:09:54,100 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/e/d/dataset_5edcb442-8f71-48fc-bf93-9638eee48f40.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/e/d/dataset_5edcb442-8f71-48fc-bf93-9638eee48f40.dat' +galaxy.jobs INFO 2024-08-30 13:09:54,130 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 89 in /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs DEBUG 2024-08-30 13:09:54,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 89 executed (196.357 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:09:56,728 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 90 +tpv.core.entities DEBUG 2024-08-30 13:09:56,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:09:56,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:09:56,771 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:09:56,791 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:09:56,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Working directory for job is: /galaxy/server/database/jobs_directory/000/90 +galaxy.jobs.runners DEBUG 2024-08-30 13:09:56,822 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [90] queued (50.550 ms) +galaxy.jobs.handler INFO 2024-08-30 13:09:56,827 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:09:56,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 90 +galaxy.jobs DEBUG 2024-08-30 13:09:56,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [90] prepared (112.124 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:09:56,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/90/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/90/registry.xml' '/galaxy/server/database/jobs_directory/000/90/upload_params.json' '105:/galaxy/server/database/objects/5/9/4/dataset_594ed40a-fa19-42e9-b639-06d673bd3371_files:/galaxy/server/database/objects/5/9/4/dataset_594ed40a-fa19-42e9-b639-06d673bd3371.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:09:57,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (90) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/90/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/90/galaxy_90.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:10:05,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 90: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:10:10,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 90 finished +galaxy.model.metadata DEBUG 2024-08-30 13:10:11,042 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 105 +galaxy.jobs INFO 2024-08-30 13:10:11,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 90 in /galaxy/server/database/jobs_directory/000/90 +galaxy.jobs DEBUG 2024-08-30 13:10:11,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 90 executed (223.816 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:10:12,204 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 91 +tpv.core.entities DEBUG 2024-08-30 13:10:12,247 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/.*, abstract=False, cores=1, mem=11.4, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:10:12,248 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:10:12,254 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:10:12,273 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:10:12,294 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Working directory for job is: /galaxy/server/database/jobs_directory/000/91 +galaxy.jobs.runners DEBUG 2024-08-30 13:10:12,304 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [91] queued (49.627 ms) +galaxy.jobs.handler INFO 2024-08-30 13:10:12,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:10:12,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 91 +galaxy.jobs DEBUG 2024-08-30 13:10:12,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [91] prepared (69.127 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:10:12,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:10:12,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:10:12,432 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:10:12,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/91/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/91/outputs/COMMAND_VERSION 2>&1; +lofreq indelqual --uniform 20 -o output.bam /galaxy/server/database/objects/5/9/4/dataset_594ed40a-fa19-42e9-b639-06d673bd3371.dat] +galaxy.jobs.runners DEBUG 2024-08-30 13:10:12,474 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (91) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/91/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/91/galaxy_91.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/91/working/output.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/91/working/output.bam" "/galaxy/server/database/objects/c/8/4/dataset_c8483965-c12d-4b4c-8cf9-4194655849bb.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:10:12,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:10:12,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-08-30 13:10:12,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:10:17,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 91: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:10:22,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 91 finished +galaxy.model.metadata DEBUG 2024-08-30 13:10:22,334 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 106 +galaxy.util WARNING 2024-08-30 13:10:22,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/8/4/dataset_c8483965-c12d-4b4c-8cf9-4194655849bb.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/8/4/dataset_c8483965-c12d-4b4c-8cf9-4194655849bb.dat' +galaxy.jobs INFO 2024-08-30 13:10:22,433 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 91 in /galaxy/server/database/jobs_directory/000/91 +galaxy.jobs DEBUG 2024-08-30 13:10:22,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 91 executed (207.292 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:10:27,694 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 92, 93 +tpv.core.entities DEBUG 2024-08-30 13:10:27,732 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:10:27,733 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:10:27,737 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:10:27,757 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:10:27,785 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Working directory for job is: /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs.runners DEBUG 2024-08-30 13:10:27,794 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [92] queued (57.103 ms) +galaxy.jobs.handler INFO 2024-08-30 13:10:27,799 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:10:27,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 92 +tpv.core.entities DEBUG 2024-08-30 13:10:27,818 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:10:27,819 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:10:27,825 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:10:27,845 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:10:27,883 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Working directory for job is: /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs.runners DEBUG 2024-08-30 13:10:27,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [93] queued (66.240 ms) +galaxy.jobs.handler INFO 2024-08-30 13:10:27,896 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:10:27,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 93 +galaxy.jobs DEBUG 2024-08-30 13:10:27,953 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [92] prepared (124.007 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:10:27,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/92/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/92/registry.xml' '/galaxy/server/database/jobs_directory/000/92/upload_params.json' '107:/galaxy/server/database/objects/c/d/6/dataset_cd62bc4b-20da-4331-9648-812a1ad14831_files:/galaxy/server/database/objects/c/d/6/dataset_cd62bc4b-20da-4331-9648-812a1ad14831.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:10:28,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (92) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/92/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/92/galaxy_92.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-08-30 13:10:28,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [93] prepared (135.517 ms) +galaxy.jobs.command_factory INFO 2024-08-30 13:10:28,088 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/93/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/93/registry.xml' '/galaxy/server/database/jobs_directory/000/93/upload_params.json' '108:/galaxy/server/database/objects/0/1/8/dataset_0189faf6-5079-43dd-a304-9b2ca6d3728d_files:/galaxy/server/database/objects/0/1/8/dataset_0189faf6-5079-43dd-a304-9b2ca6d3728d.dat'] +galaxy.jobs.runners DEBUG 2024-08-30 13:10:28,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (93) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/93/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/93/galaxy_93.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-08-30 13:10:36,692 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 92: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:10:36,712 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 93: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:10:41,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 93 finished +galaxy.jobs.runners DEBUG 2024-08-30 13:10:41,959 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 92 finished +galaxy.model.metadata DEBUG 2024-08-30 13:10:41,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 108 +galaxy.jobs INFO 2024-08-30 13:10:42,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 93 in /galaxy/server/database/jobs_directory/000/93 +galaxy.model.metadata DEBUG 2024-08-30 13:10:42,053 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 107 +galaxy.jobs INFO 2024-08-30 13:10:42,100 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 92 in /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs DEBUG 2024-08-30 13:10:42,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 93 executed (186.501 ms) +galaxy.jobs DEBUG 2024-08-30 13:10:42,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 92 executed (182.086 ms) +galaxy.jobs.handler DEBUG 2024-08-30 13:10:43,258 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 94 +tpv.core.entities DEBUG 2024-08-30 13:10:43,304 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/.*, abstract=False, cores=5, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-08-30 13:10:43,305 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-08-30 13:10:43,311 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-08-30 13:10:43,329 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-08-30 13:10:43,374 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Working directory for job is: /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs.runners DEBUG 2024-08-30 13:10:43,387 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [94] queued (75.900 ms) +galaxy.jobs.handler INFO 2024-08-30 13:10:43,394 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-08-30 13:10:43,396 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 94 +galaxy.jobs DEBUG 2024-08-30 13:10:43,533 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [94] prepared (114.767 ms) +galaxy.tool_util.deps.containers INFO 2024-08-30 13:10:43,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:10:43,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1: mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:10:43,742 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-08-30 13:10:43,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/94/tool_script.sh] for tool command [ln -s /galaxy/server/database/objects/c/d/6/dataset_cd62bc4b-20da-4331-9648-812a1ad14831.dat reference.fa && ln -s /galaxy/server/database/objects/0/1/8/dataset_0189faf6-5079-43dd-a304-9b2ca6d3728d.dat query.fa && nucmer -b '200' -c '65' -D '5' -d '0.12' -g '90' -l '20' -L '0' --threads "${GALAXY_SLOTS:-1}" 'reference.fa' 'query.fa' && mummerplot -R '/galaxy/server/database/objects/c/d/6/dataset_cd62bc4b-20da-4331-9648-812a1ad14831.dat' -Q '/galaxy/server/database/objects/0/1/8/dataset_0189faf6-5079-43dd-a304-9b2ca6d3728d.dat' -b '20' -s 'small' -terminal png -title 'Title' 'out.delta' && gnuplot < out.gp] +galaxy.jobs.runners DEBUG 2024-08-30 13:10:43,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (94) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/94/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/94/galaxy_94.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/94/working/out.delta" ] ; then cp "/galaxy/server/database/jobs_directory/000/94/working/out.delta" "/galaxy/server/database/objects/e/7/8/dataset_e7826b1d-ffbd-482b-bf3c-b70b8f7a2288.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/94/working/out.png" ] ; then cp "/galaxy/server/database/jobs_directory/000/94/working/out.png" "/galaxy/server/database/objects/0/9/f/dataset_09ff0a69-0d0b-4066-961a-2b1af50055f8.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-08-30 13:10:43,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-08-30 13:10:43,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1: mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c +galaxy.tool_util.deps.containers INFO 2024-08-30 13:10:43,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-08-30 13:11:10,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 94: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-08-30 13:11:15,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 94 finished +galaxy.model.metadata DEBUG 2024-08-30 13:11:15,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 110 +galaxy.model.metadata DEBUG 2024-08-30 13:11:15,468 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 109 +galaxy.jobs INFO 2024-08-30 13:11:15,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 94 in /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs DEBUG 2024-08-30 13:11:15,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 94 executed (185.478 ms) diff --git a/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/jobs.txt b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/jobs.txt new file mode 100644 index 000000000..5171d1d15 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/jobs.txt @@ -0,0 +1,94 @@ +ea3e808f13e0175c ok 2024-08-30T13:11:15.526788 toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1 +5835e2fe3b1be6c6 ok 2024-08-30T13:10:42.104152 upload1 +af686d0530be6436 ok 2024-08-30T13:10:42.040975 upload1 +38e5943f3cf9e7a1 ok 2024-08-30T13:10:22.437086 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 +ba18cd8c087f0154 ok 2024-08-30T13:10:11.135929 upload1 +915a352ef8644fda ok 2024-08-30T13:09:54.134190 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 +ab2873333ea7b271 ok 2024-08-30T13:09:43.154821 upload1 +75468927e1e47623 ok 2024-08-30T13:09:42.981563 upload1 +a570955de08d43f9 ok 2024-08-30T13:09:24.562907 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 +6438f3d32c4013c9 ok 2024-08-30T13:09:07.311236 upload1 +6e95eddc84cda40d ok 2024-08-30T13:08:47.876456 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +21383bfca5be1aac ok 2024-08-30T13:08:35.937281 upload1 +44901ea38dea194c ok 2024-08-30T13:08:18.490621 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +0ff3cf4cdd53f073 ok 2024-08-30T13:08:07.497046 upload1 +7a3a784002d9b2e4 ok 2024-08-30T13:07:49.918245 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +c20446b95cd50d61 ok 2024-08-30T13:07:38.950211 upload1 +18cc197ba26e8e47 ok 2024-08-30T13:07:22.505998 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +7cf1947c1168a2c0 ok 2024-08-30T13:07:10.638251 upload1 +f4f3e423337ae3b0 ok 2024-08-30T13:06:53.044773 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +2d284e114fa37175 ok 2024-08-30T13:06:41.787283 upload1 +51e554051ef9c10a ok 2024-08-30T13:06:24.830369 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +fbbbf1f96f8e5488 ok 2024-08-30T13:06:12.403702 upload1 +e0b49637d014491c ok 2024-08-30T13:05:54.201725 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +b3563ccd5e1e3ab8 ok 2024-08-30T13:05:42.993020 upload1 +5ea0491d7d9d49ff ok 2024-08-30T13:05:23.941401 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 +b9dde3d46c4379df ok 2024-08-30T13:05:11.995272 upload1 +85c44b3c6b9e7586 ok 2024-08-30T13:05:10.981739 upload1 +d9f9da59e3f2406f ok 2024-08-30T13:04:54.369038 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 +b21d89599c6459c7 ok 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beta.kubernetes.io/instance-type=e2-custom-20-81920 + beta.kubernetes.io/os=linux + cloud.google.com/gke-boot-disk=pd-balanced + cloud.google.com/gke-container-runtime=containerd + cloud.google.com/gke-cpu-scaling-level=20 + cloud.google.com/gke-logging-variant=DEFAULT + cloud.google.com/gke-max-pods-per-node=110 + cloud.google.com/gke-nodepool=default-pool + cloud.google.com/gke-os-distribution=cos + cloud.google.com/gke-provisioning=standard + cloud.google.com/gke-stack-type=IPV4 + cloud.google.com/machine-family=e2 + cloud.google.com/private-node=false + failure-domain.beta.kubernetes.io/region=us-east1 + failure-domain.beta.kubernetes.io/zone=us-east1-b + kubernetes.io/arch=amd64 + kubernetes.io/hostname=gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq + kubernetes.io/os=linux + node.kubernetes.io/instance-type=e2-custom-20-81920 + topology.gke.io/zone=us-east1-b + topology.kubernetes.io/region=us-east1 + topology.kubernetes.io/zone=us-east1-b +Annotations: container.googleapis.com/instance_id: 537935981085196976 + csi.volume.kubernetes.io/nodeid: + {"cvmfs.csi.cern.ch":"gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq","pd.csi.storage.gke.io":"projects/anvil-and-terra-development/zo... + node.alpha.kubernetes.io/ttl: 0 + node.gke.io/last-applied-node-labels: + cloud.google.com/gke-boot-disk=pd-balanced,cloud.google.com/gke-container-runtime=containerd,cloud.google.com/gke-cpu-scaling-level=20,clo... + node.gke.io/last-applied-node-taints: + volumes.kubernetes.io/controller-managed-attach-detach: true +CreationTimestamp: Fri, 30 Aug 2024 12:39:22 +0000 +Taints: +Unschedulable: false +Lease: + HolderIdentity: gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq + AcquireTime: + RenewTime: Fri, 30 Aug 2024 13:11:49 +0000 +Conditions: + Type Status LastHeartbeatTime LastTransitionTime Reason Message + ---- ------ ----------------- ------------------ ------ ------- + DeprecatedConfigsFieldInContainerdConfiguration False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 DeprecatedConfigsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'configs' field in containerd's config + DeprecatedOtherContainerdFeatures False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 DeprecatedOtherContainerdFeaturesNotDetected No deprecation risk: did not find any deprecations other than 3 configs fields (auths/configs/mirrors), pulling schema v1 images and using v1alpha2 CRI. + DeprecatedAuthsFieldInContainerdConfiguration False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 DeprecatedAuthsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'auths' field in containerd's config + FrequentUnregisterNetDevice False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 NoFrequentUnregisterNetDevice node is functioning properly + FrequentContainerdRestart False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 NoFrequentContainerdRestart containerd is functioning properly + ReadonlyFilesystem False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 FilesystemIsNotReadOnly Filesystem is not read-only + FrequentDockerRestart False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 NoFrequentDockerRestart docker is functioning properly + DeprecatedMirrorsFieldInContainerdConfiguration False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 DeprecatedMirrorsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'mirrors' field in containerd's config + FrequentKubeletRestart False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 NoFrequentKubeletRestart kubelet is functioning properly + DeprecatedPullingSchemaV1Image False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 DeprecatedPullingSchemaV1ImageDetected No deprecation risk: did not pull any schema v1 images + DeprecatedUsingV1Alpha2Cri False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 DeprecatedUsingV1Alpha2CriNotDetected No deprecation risk: did not use v1alpha2 CRI + KernelDeadlock False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 KernelHasNoDeadlock kernel has no deadlock + CorruptDockerOverlay2 False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 NoCorruptDockerOverlay2 docker overlay2 is functioning properly + SysctlChanged False Fri, 30 Aug 2024 13:09:25 +0000 Fri, 30 Aug 2024 12:39:22 +0000 SysctlNotChanged Default sysctls are in effect, no unexpected sysctl changes + NetworkUnavailable False Fri, 30 Aug 2024 12:39:23 +0000 Fri, 30 Aug 2024 12:39:23 +0000 RouteCreated NodeController create implicit route + MemoryPressure False Fri, 30 Aug 2024 13:11:09 +0000 Fri, 30 Aug 2024 12:38:56 +0000 KubeletHasSufficientMemory kubelet has sufficient memory available + DiskPressure False Fri, 30 Aug 2024 13:11:09 +0000 Fri, 30 Aug 2024 12:38:56 +0000 KubeletHasNoDiskPressure kubelet has no disk pressure + PIDPressure False Fri, 30 Aug 2024 13:11:09 +0000 Fri, 30 Aug 2024 12:38:56 +0000 KubeletHasSufficientPID kubelet has sufficient PID available + Ready True Fri, 30 Aug 2024 13:11:09 +0000 Fri, 30 Aug 2024 12:39:42 +0000 KubeletReady kubelet is posting ready status. AppArmor enabled +Addresses: + InternalIP: 10.142.0.15 + ExternalIP: 34.138.238.104 + Hostname: gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq +Capacity: + cpu: 20 + ephemeral-storage: 98831908Ki + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 82369080Ki + pods: 110 +Allocatable: + cpu: 19880m + ephemeral-storage: 47060071478 + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 75554360Ki + pods: 110 +System Info: + Machine ID: 563896da24aafd38f8d363fdd5b7e399 + System UUID: 563896da-24aa-fd38-f8d3-63fdd5b7e399 + Boot ID: ffab6337-8b86-42a6-b7e2-fab218bd8d17 + Kernel Version: 6.1.85+ + OS Image: Container-Optimized OS from Google + Operating System: linux + Architecture: amd64 + Container Runtime Version: containerd://1.7.15 + Kubelet Version: v1.28.12-gke.1052000 + Kube-Proxy Version: v1.28.12-gke.1052000 +PodCIDR: 10.32.0.0/24 +PodCIDRs: 10.32.0.0/24 +ProviderID: gce://anvil-and-terra-development/us-east1-b/gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq +Non-terminated Pods: (26 in total) + Namespace Name CPU Requests CPU Limits Memory Requests Memory Limits Age + --------- ---- ------------ ---------- --------------- ------------- --- + gmp-system collector-9gfxh 5m (0%) 0 (0%) 36M (0%) 3032M (3%) 32m + gmp-system gmp-operator-6c694668bf-lljkr 1m (0%) 0 (0%) 16M (0%) 2G (2%) 33m + kube-system event-exporter-gke-58c99c7869-rjpkx 3m (0%) 0 (0%) 100Mi (0%) 0 (0%) 33m + kube-system fluentbit-gke-5vkb4 100m (0%) 0 (0%) 200Mi (0%) 500Mi (0%) 32m + kube-system gke-metrics-agent-kcg7w 9m (0%) 0 (0%) 110Mi (0%) 110Mi (0%) 32m + kube-system konnectivity-agent-54cb695598-bcvkm 15m (0%) 0 (0%) 60Mi (0%) 155Mi (0%) 33m + kube-system konnectivity-agent-autoscaler-697695f8c5-p8w2b 10m (0%) 0 (0%) 10M (0%) 0 (0%) 33m + kube-system kube-dns-6f955b858b-4k47x 260m (1%) 0 (0%) 110Mi (0%) 210Mi (0%) 33m + kube-system kube-dns-autoscaler-755c7dfdf5-mwqxt 20m (0%) 0 (0%) 10Mi (0%) 0 (0%) 33m + kube-system kube-proxy-gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq 100m (0%) 0 (0%) 0 (0%) 0 (0%) 31m + kube-system l7-default-backend-85b45d5c78-56fmr 10m (0%) 0 (0%) 20Mi (0%) 0 (0%) 33m + kube-system metrics-server-v0.7.0-7787fd6556-d4c5j 48m (0%) 43m (0%) 105Mi (0%) 355Mi (0%) 32m + kube-system pdcsi-node-vzw8v 10m (0%) 0 (0%) 20Mi (0%) 100Mi (0%) 32m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-cvmfscsi-controllerplugin-6f5558f48ctg24l 0 (0%) 0 (0%) 0 (0%) 0 (0%) 30m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-cvmfscsi-nodeplugin-jmls8 0 (0%) 0 (0%) 0 (0%) 0 (0%) 25m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-galaxy-celery-5cf5676b96-pf2n9 500m (2%) 2 (10%) 2G (2%) 8G (10%) 29m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-galaxy-celery-beat-7944fd8f55-cs6c2 500m (2%) 2 (10%) 2G (2%) 8G (10%) 29m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-galaxy-galaxy-postgres-0 250m (1%) 0 (0%) 256Mi (0%) 0 (0%) 29m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-galaxy-job-0-6c546cdcbc-7wm27 500m (2%) 2 (10%) 2G (2%) 8G (10%) 29m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-galaxy-nginx-8f6857dc7-4s4x9 100m (0%) 2 (10%) 500M (0%) 3G (3%) 29m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-galaxy-rabbitmq-server-server-0 1 (5%) 2 (10%) 2Gi (2%) 2Gi (2%) 29m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-galaxy-web-85fd97c6b7-fvrmp 500m (2%) 2 (10%) 2G (2%) 8G (10%) 29m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-galaxy-workflow-78c5464fdf-99fgl 500m (2%) 2 (10%) 2G (2%) 8G (10%) 29m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-nfs-0 0 (0%) 0 (0%) 0 (0%) 0 (0%) 30m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-rabbitmq-b9968c466-mpnfp 0 (0%) 0 (0%) 0 (0%) 0 (0%) 30m + prod-24-08-30-12-32-1 prod-24-08-30-12-32-1-rabbitmq-messaging-topology-operator22dl2 0 (0%) 0 (0%) 0 (0%) 0 (0%) 30m +Allocated resources: + (Total limits may be over 100 percent, i.e., overcommitted.) + Resource Requests Limits + -------- -------- ------ + cpu 4441m (22%) 14043m (70%) + memory 13748622464 (17%) 51678947328 (66%) + ephemeral-storage 35Gi (79%) 200Gi (456%) + hugepages-1Gi 0 (0%) 0 (0%) + hugepages-2Mi 0 (0%) 0 (0%) +Events: + Type Reason Age From Message + ---- ------ ---- ---- ------- + Normal Starting 32m kube-proxy + Normal Starting 36m kubelet Starting kubelet. + Warning InvalidDiskCapacity 36m kubelet invalid capacity 0 on image filesystem + Normal NodeAllocatableEnforced 36m kubelet Updated Node Allocatable limit across pods + Normal NodeHasNoDiskPressure 34m (x7 over 36m) kubelet Node gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq status is now: NodeHasNoDiskPressure + Normal NodeHasSufficientPID 34m (x7 over 36m) kubelet Node gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq status is now: NodeHasSufficientPID + Normal NodeHasSufficientMemory 33m (x8 over 36m) kubelet Node gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq status is now: NodeHasSufficientMemory + Warning NodeRegistrationCheckerStart 32m node-registration-checker-monitor Fri Aug 30 12:35:07 UTC 2024 - ** Starting Node Registration Checker ** + Normal Synced 32m cloud-node-controller Node synced successfully + Normal RegisteredNode 32m node-controller Node gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq event: Registered Node gke-prod-24-08-30-12-32-default-pool-f6eae4d0-39rq in Controller + Warning NodeRegistrationCheckerDidNotRunChecks 29m node-registration-checker-monitor Fri Aug 30 12:42:08 UTC 2024 - ** Node ready and registered. ** diff --git a/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/results.html b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/results.html new file mode 100644 index 000000000..a4d54a7be --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
+
+
+
+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/results.json b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/results.json new file mode 100644 index 000000000..01dc83c68 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 40, "errors": 0, "failures": 9, "skips": 0}, "tests": [{"id": "bcftools_cnv/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_cnv", "tool_version": "1.10", "test_index": 0, "time_seconds": 50.307536363601685, "inputs": {"input_file": {"src": "hda", "id": "5302a10e39b38a93"}}, "job": {"model_class": "Job", "id": "38e0158e5ebfa1e2", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:57:01.222413", "create_time": "2024-08-30T12:56:27.200146", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10", "history_id": "156c4392fa643bca", "external_id": "gxy-p9jfx", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/a/5/dataset_fa5c2641-183c-415d-9a5b-764b9dec32d7.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp -p 0 --aberrant \"1.0,1.0\" --BAF-weight 1.0 --BAF-dev \"0.04,0.04\" --LRR-weight 0.2 --LRR-dev \"0.2,0.2\" --LRR-smooth-win 10 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/0/7/6/dataset_0769d0b8-f60d-4d5d-94da-f071cb821c26.dat' && mv cnv_tmp/summary.*.tab '/galaxy/server/database/objects/d/8/a/dataset_d8aa9ded-1390-495a-9a76-aa639af0d205.dat' && (echo 'Copy-number variation plots (bcftools cnv)' > /galaxy/server/database/objects/a/2/a/dataset_a2a2705e-2b98-4a45-855f-12a54f0a9486.dat; for plot in cnv_tmp/*.png; do [ -f \"$plot\" ] || break; echo '
> /galaxy/server/database/objects/a/2/a/dataset_a2a2705e-2b98-4a45-855f-12a54f0a9486.dat; python -m base64 $plot >> /galaxy/server/database/objects/a/2/a/dataset_a2a2705e-2b98-4a45-855f-12a54f0a9486.dat; echo '\" />
' >> /galaxy/server/database/objects/a/2/a/dataset_a2a2705e-2b98-4a45-855f-12a54f0a9486.dat; done; echo '' >> /galaxy/server/database/objects/a/2/a/dataset_a2a2705e-2b98-4a45-855f-12a54f0a9486.dat;)", "traceback": null, "params": {"query_sample": null, "control_sample": null, "AF_file": null, "plotting": "{\"__current_case__\": 0, \"generate_plots\": \"all\", \"plot_threshold\": \"0\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}", "sec_hmm": "{\"aberrant_control\": \"1.0\", \"aberrant_optimization\": {\"__current_case__\": 0, \"do_optimize\": \"no\"}, \"aberrant_query\": \"1.0\", \"err_prob\": \"0.0001\", \"same_prob\": \"0.5\", \"score_usage\": {\"__current_case__\": 0, \"baf_dev_control\": \"0.04\", \"baf_dev_query\": \"0.04\", \"baf_weight\": \"1.0\", \"compute_on\": \"baf+lrr\", \"lrr_dev_control\": \"0.2\", \"lrr_dev_query\": \"0.2\", \"lrr_smooth_win\": \"10\", \"lrr_weight\": \"0.2\"}, \"xy_prob\": \"1e-09\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"vcf\""}, "inputs": {"input_file": {"id": "5302a10e39b38a93", "src": "hda", "uuid": "fa5c2641-183c-415d-9a5b-764b9dec32d7"}}, "outputs": {"output_summary": {"id": "a629f136fcaf7040", "src": "hda", "uuid": "d8aa9ded-1390-495a-9a76-aa639af0d205"}, "output_plots": {"id": "ae94dc40a80201c8", "src": "hda", "uuid": "a2a2705e-2b98-4a45-855f-12a54f0a9486"}, "output_cn": {"id": "a27489f36aeff263", "src": "hda", "uuid": "0769d0b8-f60d-4d5d-94da-f071cb821c26"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of lines: total/processed: 184/184\n", "job_stdout": "", "job_stderr": "", "stderr": "Number of lines: total/processed: 184/184\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:56:46", "plugin": "core", "name": "end_epoch", "raw_value": "1725022606.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:56:43", "plugin": "core", "name": "start_epoch", "raw_value": "1725022603.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_cnv/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_cnv", "tool_version": "1.10", "test_index": 1, "time_seconds": 26.824493885040283, "inputs": {"input_file": {"src": "hda", "id": "d7a42a5aa611aaed"}, "plotting|generate_plots": "none"}, "job": {"model_class": "Job", "id": "0a2d17a5e5658f2e", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:57:28.283281", "create_time": "2024-08-30T12:57:17.428673", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10", "history_id": "156c4392fa643bca", "external_id": "gxy-fpznh", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/a/5/dataset_8a5edff4-5721-4aee-b148-fed33af01781.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp --aberrant \"1.0,1.0\" --BAF-weight 1.0 --BAF-dev \"0.04,0.04\" --LRR-weight 0.2 --LRR-dev \"0.2,0.2\" --LRR-smooth-win 10 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/d/3/b/dataset_d3bf143f-6240-4646-80a1-007581f820b9.dat' && mv cnv_tmp/summary.*.tab '/galaxy/server/database/objects/1/c/c/dataset_1cc76856-26db-4b2d-931d-d15cd53421ee.dat'", "traceback": null, "params": {"query_sample": null, "control_sample": null, "AF_file": null, "plotting": "{\"__current_case__\": 2, \"generate_plots\": \"none\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}", "sec_hmm": "{\"aberrant_control\": \"1.0\", \"aberrant_optimization\": {\"__current_case__\": 0, \"do_optimize\": \"no\"}, \"aberrant_query\": \"1.0\", \"err_prob\": \"0.0001\", \"same_prob\": \"0.5\", \"score_usage\": {\"__current_case__\": 0, \"baf_dev_control\": \"0.04\", \"baf_dev_query\": \"0.04\", \"baf_weight\": \"1.0\", \"compute_on\": \"baf+lrr\", \"lrr_dev_control\": \"0.2\", \"lrr_dev_query\": \"0.2\", \"lrr_smooth_win\": \"10\", \"lrr_weight\": \"0.2\"}, \"xy_prob\": \"1e-09\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"vcf\""}, "inputs": {"input_file": {"id": "d7a42a5aa611aaed", "src": "hda", "uuid": "8a5edff4-5721-4aee-b148-fed33af01781"}}, "outputs": {"output_cn": {"id": "3a9d800057b68c29", "src": "hda", "uuid": "d3bf143f-6240-4646-80a1-007581f820b9"}, "output_summary": {"id": "7e2dda28cca230dc", "src": "hda", "uuid": "1cc76856-26db-4b2d-931d-d15cd53421ee"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of lines: total/processed: 184/184\n", "job_stdout": "", "job_stderr": "", "stderr": "Number of lines: total/processed: 184/184\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 12:57:19", "plugin": "core", "name": "end_epoch", "raw_value": "1725022639.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:57:19", "plugin": "core", "name": "start_epoch", "raw_value": "1725022639.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_cnv/1.10-2", "has_data": true, "data": {"tool_id": "bcftools_cnv", "tool_version": "1.10", "test_index": 2, "time_seconds": 31.480050563812256, "inputs": {"input_file": {"src": "hda", "id": "849d1de06f90547b"}, "query_sample": "test", "control_sample": "test"}, "job": {"model_class": "Job", "id": "9de808f54edb8972", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:57:59.870304", "create_time": "2024-08-30T12:57:44.946372", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10", "history_id": "156c4392fa643bca", "external_id": "gxy-dckc4", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/f/d/dataset_4fd6a427-8363-42f8-8067-838469bfbf0a.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp -c 'test' -s 'test' -p 0 --aberrant \"1.0,1.0\" --BAF-weight 1.0 --BAF-dev \"0.04,0.04\" --LRR-weight 0.2 --LRR-dev \"0.2,0.2\" --LRR-smooth-win 10 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/9/a/a/dataset_9aab51e9-e62d-45b3-9601-d81a62dbe528.dat' && mv cnv_tmp/summary.tab '/galaxy/server/database/objects/a/1/c/dataset_a1c47531-bbb4-42b2-8b85-4b3d651a867a.dat' && (echo 'Copy-number variation plots (bcftools cnv)' > /galaxy/server/database/objects/9/8/7/dataset_98793b8d-c28b-4266-8acf-e51f3d920cc0.dat; for plot in cnv_tmp/*.png; do [ -f \"$plot\" ] || break; echo '
> /galaxy/server/database/objects/9/8/7/dataset_98793b8d-c28b-4266-8acf-e51f3d920cc0.dat; python -m base64 $plot >> /galaxy/server/database/objects/9/8/7/dataset_98793b8d-c28b-4266-8acf-e51f3d920cc0.dat; echo '\" />
' >> /galaxy/server/database/objects/9/8/7/dataset_98793b8d-c28b-4266-8acf-e51f3d920cc0.dat; done; echo '' >> /galaxy/server/database/objects/9/8/7/dataset_98793b8d-c28b-4266-8acf-e51f3d920cc0.dat;)", "traceback": null, "params": {"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "query_sample": "\"test\"", "control_sample": "\"test\"", "AF_file": null, "plotting": "{\"__current_case__\": 0, \"generate_plots\": \"all\", \"plot_threshold\": \"0\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}", "sec_hmm": "{\"aberrant_control\": \"1.0\", \"aberrant_optimization\": {\"__current_case__\": 0, \"do_optimize\": \"no\"}, \"aberrant_query\": \"1.0\", \"err_prob\": \"0.0001\", \"same_prob\": \"0.5\", \"score_usage\": {\"__current_case__\": 0, \"baf_dev_control\": \"0.04\", \"baf_dev_query\": \"0.04\", \"baf_weight\": \"1.0\", \"compute_on\": \"baf+lrr\", \"lrr_dev_control\": \"0.2\", \"lrr_dev_query\": \"0.2\", \"lrr_smooth_win\": \"10\", \"lrr_weight\": \"0.2\"}, \"xy_prob\": \"1e-09\"}", "__input_ext": "\"vcf\""}, "inputs": {"input_file": {"id": "849d1de06f90547b", "src": "hda", "uuid": "4fd6a427-8363-42f8-8067-838469bfbf0a"}}, "outputs": {"output_cn": {"id": "57d6525ceb3c7ff6", "src": "hda", "uuid": "9aab51e9-e62d-45b3-9601-d81a62dbe528"}, "output_plots": {"id": "57d4cb6a07ed3fc2", "src": "hda", "uuid": "98793b8d-c28b-4266-8acf-e51f3d920cc0"}, "output_summary": {"id": "6ba9cd0931299b66", "src": "hda", "uuid": "a1c47531-bbb4-42b2-8b85-4b3d651a867a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of lines: total/processed: 184/184\n", "job_stdout": "", "job_stderr": "", "stderr": "Number of lines: total/processed: 184/184\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:57:51", "plugin": "core", "name": "end_epoch", "raw_value": "1725022671.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:57:47", "plugin": "core", "name": "start_epoch", "raw_value": "1725022667.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_cnv/1.10-3", "has_data": true, "data": {"tool_id": "bcftools_cnv", "tool_version": "1.10", "test_index": 3, "time_seconds": 28.185099840164185, "inputs": {"input_file": {"src": "hda", "id": "ecde87cc004b1c6a"}, "plotting|generate_plots": "none", "sec_hmm|score_usage|compute_on": "baf"}, "job": {"model_class": "Job", "id": "019b97a522616e6d", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:58:28.149878", "create_time": "2024-08-30T12:58:16.366909", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10", "history_id": "156c4392fa643bca", "external_id": "gxy-qpzd9", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/a/5/f/dataset_a5f78e95-6f79-49dc-b010-352d9e643601.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp --aberrant \"1.0,1.0\" --BAF-weight 1 --BAF-dev \"0.04,0.04\" --LRR-weight 0 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/b/4/a/dataset_b4ac5087-c77a-4095-ade6-6187f6f3c15d.dat' && mv cnv_tmp/summary.*.tab '/galaxy/server/database/objects/c/8/4/dataset_c840bf3a-243c-4a67-a099-8c4d772e01e3.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_hmm": "{\"aberrant_control\": \"1.0\", \"aberrant_optimization\": {\"__current_case__\": 0, \"do_optimize\": \"no\"}, \"aberrant_query\": \"1.0\", \"err_prob\": \"0.0001\", \"same_prob\": \"0.5\", \"score_usage\": {\"__current_case__\": 1, \"baf_dev_control\": \"0.04\", \"baf_dev_query\": \"0.04\", \"baf_weight\": \"1\", \"compute_on\": \"baf\", \"lrr_weight\": \"0\"}, \"xy_prob\": \"1e-09\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}", "plotting": "{\"__current_case__\": 2, \"generate_plots\": \"none\"}", "AF_file": null, "control_sample": null, "query_sample": null}, "inputs": {"input_file": {"id": "ecde87cc004b1c6a", "src": "hda", "uuid": "a5f78e95-6f79-49dc-b010-352d9e643601"}}, "outputs": {"output_cn": {"id": "ca0dbf2286d6aab6", "src": "hda", "uuid": "b4ac5087-c77a-4095-ade6-6187f6f3c15d"}, "output_summary": {"id": "1a47f051541ad4a1", "src": "hda", "uuid": "c840bf3a-243c-4a67-a099-8c4d772e01e3"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of lines: total/processed: 184/184\n", "job_stdout": "", "job_stderr": "", "stderr": "Number of lines: total/processed: 184/184\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 12:58:18", "plugin": "core", "name": "end_epoch", "raw_value": "1725022698.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:58:18", "plugin": "core", "name": "start_epoch", "raw_value": "1725022698.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_roh/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_roh", "tool_version": "1.10", "test_index": 0, "time_seconds": 34.53428769111633, "inputs": {"input_file": {"src": "hda", "id": "8bcd04047caac1fc"}, "sec_general|AF_dflt": "0.4", "sec_general|GTs_only": "30"}, "job": {"model_class": "Job", "id": "5302a10e39b38a93", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:59:03.869591", "create_time": "2024-08-30T12:58:46.900069", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10", "history_id": "156c4392fa643bca", "external_id": "gxy-zk47k", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/9/0/e/dataset_90e25232-e913-4060-a42e-b369ccbf38a1.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools roh --AF-dflt \"0.4\" --GTs-only \"30.0\" --hw-to-az \"6.7e-08\" --az-to-hw \"5e-09\" input.vcf.gz > '/galaxy/server/database/objects/9/1/6/dataset_91661122-93ee-4b77-a728-da66819db87b.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": null, "sec_hmm": "{\"az_to_hw\": \"5e-09\", \"hw_to_az\": \"6.7e-08\", \"viterbi_training\": false}", "sec_general": "{\"AF_dflt\": \"0.4\", \"AF_file\": null, \"AF_tag\": \"\", \"GTs_only\": \"30.0\", \"buffer_overlap\": \"\", \"buffer_size\": \"\", \"estimate_AF\": null, \"genetic_map\": null, \"rec_rate\": \"\", \"sample\": null, \"skip_indels\": false}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_file": {"id": "8bcd04047caac1fc", "src": "hda", "uuid": "90e25232-e913-4060-a42e-b369ccbf38a1"}}, "outputs": {"output_file": {"id": "e0569ebde28ee8e6", "src": "hda", "uuid": "91661122-93ee-4b77-a728-da66819db87b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of target samples: 1\nNumber of --estimate-AF samples: 0\nNumber of sites in the buffer/overlap: unlimited\nNumber of lines total/processed: 8890/8888\nNumber of lines filtered/no AF/not biallelic/dup: 0/0/1/1\n", "job_stdout": "", "job_stderr": "", "stderr": "Number of target samples: 1\nNumber of --estimate-AF samples: 0\nNumber of sites in the buffer/overlap: unlimited\nNumber of lines total/processed: 8890/8888\nNumber of lines filtered/no AF/not biallelic/dup: 0/0/1/1\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:58:53", "plugin": "core", "name": "end_epoch", "raw_value": "1725022733.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:58:52", "plugin": "core", "name": "start_epoch", "raw_value": "1725022732.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_roh/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_roh", "tool_version": "1.10", "test_index": 1, "time_seconds": 28.647672414779663, "inputs": {"input_file": {"src": "hda", "id": "df4be1d1e9033ceb"}, "sec_general|AF_dflt": "0.4", "sec_general|GTs_only": "30", "output_type": "r"}, "job": {"model_class": "Job", "id": "a629f136fcaf7040", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:59:32.818666", "create_time": "2024-08-30T12:59:21.540362", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10", "history_id": "156c4392fa643bca", "external_id": "gxy-ttrst", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/a/0/9/dataset_a092ad03-0b78-4e9e-8237-00748efe3dc8.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools roh --AF-dflt \"0.4\" --GTs-only \"30.0\" --hw-to-az \"6.7e-08\" --az-to-hw \"5e-09\" --output-type r input.vcf.gz > '/galaxy/server/database/objects/a/b/0/dataset_ab0c362c-9692-4519-932e-dad2c0b4f998.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"r\"", "sec_hmm": "{\"az_to_hw\": \"5e-09\", \"hw_to_az\": \"6.7e-08\", \"viterbi_training\": false}", "sec_general": "{\"AF_dflt\": \"0.4\", \"AF_file\": null, \"AF_tag\": \"\", \"GTs_only\": \"30.0\", \"buffer_overlap\": \"\", \"buffer_size\": \"\", \"estimate_AF\": null, \"genetic_map\": null, \"rec_rate\": \"\", \"sample\": null, \"skip_indels\": false}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_file": {"id": "df4be1d1e9033ceb", "src": "hda", "uuid": "a092ad03-0b78-4e9e-8237-00748efe3dc8"}}, "outputs": {"output_file": {"id": "d0f64fa7dfce59dc", "src": "hda", "uuid": "ab0c362c-9692-4519-932e-dad2c0b4f998"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of target samples: 1\nNumber of --estimate-AF samples: 0\nNumber of sites in the buffer/overlap: unlimited\nNumber of lines total/processed: 8890/8888\nNumber of lines filtered/no AF/not biallelic/dup: 0/0/1/1\n", "job_stdout": "", "job_stderr": "", "stderr": "Number of target samples: 1\nNumber of --estimate-AF samples: 0\nNumber of sites in the buffer/overlap: unlimited\nNumber of lines total/processed: 8890/8888\nNumber of lines filtered/no AF/not biallelic/dup: 0/0/1/1\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 12:59:23", "plugin": "core", "name": "end_epoch", "raw_value": "1725022763.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:59:23", "plugin": "core", "name": "start_epoch", "raw_value": "1725022763.0000000"}, {"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": "deeptools_bam_coverage/3.3.2.0.0-0", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 0, "time_seconds": 28.626880168914795, "inputs": {"bamInput": {"src": "hda", "id": "a570955de08d43f9"}, "binSize": "10", "scaling|type": "no", "outFileFormat": "bigwig", "advancedOpt|showAdvancedOpt": "no"}, "job": {"model_class": "Job", "id": "e0b49637d014491c", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:05:54.201725", "create_time": "2024-08-30T13:05:43.253677", "galaxy_version": "23.1", "command_version": "bamCoverage 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "history_id": "156c4392fa643bca", "external_id": "gxy-vzgdh", "command_line": "ln -s '/galaxy/server/database/objects/2/4/1/dataset_24199aa4-d69a-4199-8d54-5aec551c087d.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/3/6/8/metadata_3688c290-7b37-43e5-af69-fbdff8bae1ad.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/1/6/7/dataset_167b4e7b-54b1-4fbd-9556-c163ab456185.dat' --outFileFormat 'bigwig' --binSize 10", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "region": "\"\"", "exactScaling": "false", "outFileFormat": "\"bigwig\"", "scaling": "{\"__current_case__\": 3, \"type\": \"no\"}", "binSize": "\"10\""}, "inputs": {"bamInput": {"id": "a570955de08d43f9", "src": "hda", "uuid": "24199aa4-d69a-4199-8d54-5aec551c087d"}}, "outputs": {"outFileName": {"id": "ab2873333ea7b271", "src": "hda", "uuid": "167b4e7b-54b1-4fbd-9556-c163ab456185"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "bamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stderr": "bamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 13:05:45", "plugin": "core", "name": "end_epoch", "raw_value": "1725023145.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:05:45", "plugin": "core", "name": "start_epoch", "raw_value": "1725023145.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-1", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 1, "time_seconds": 30.66047692298889, "inputs": {"bamInput": {"src": "hda", "id": "75468927e1e47623"}, "binSize": "10", "scaling|effectiveGenomeSize|effectiveGenomeSize": "2451960000", "scaling|effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "outFileFormat": "bigwig", "advancedOpt|showAdvancedOpt": "no"}, "job": {"model_class": "Job", "id": "51e554051ef9c10a", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:06:24.830369", "create_time": "2024-08-30T13:06:12.663610", "galaxy_version": "23.1", "command_version": "bamCoverage 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "history_id": "156c4392fa643bca", "external_id": "gxy-t4g2p", "command_line": "ln -s '/galaxy/server/database/objects/6/2/2/dataset_62204f6e-8047-45b5-a698-b68e50bac7d5.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/b/2/b/metadata_b2b49118-b465-417d-b858-f1f54d33a292.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/4/6/0/dataset_4609bcf0-2af2-46c7-b164-a2589c3c4fae.dat' --outFileFormat 'bigwig' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "region": "\"\"", "exactScaling": "false", "outFileFormat": "\"bigwig\"", "scaling": "{\"__current_case__\": 4, \"effectiveGenomeSize\": {\"__current_case__\": 0, \"effectiveGenomeSize\": \"2451960000\", \"effectiveGenomeSize_opt\": \"specific\"}, \"type\": \"1x\"}", "binSize": "\"10\""}, "inputs": {"bamInput": {"id": "75468927e1e47623", "src": "hda", "uuid": "62204f6e-8047-45b5-a698-b68e50bac7d5"}}, "outputs": {"outFileName": {"id": "915a352ef8644fda", "src": "hda", "uuid": "4609bcf0-2af2-46c7-b164-a2589c3c4fae"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 13:06:15", "plugin": "core", "name": "end_epoch", "raw_value": "1725023175.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:06:15", "plugin": "core", "name": "start_epoch", "raw_value": "1725023175.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-2", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 2, "time_seconds": 28.162803411483765, "inputs": {"bamInput": {"src": "hda", "id": "ba18cd8c087f0154"}, "binSize": "10", "scaling|effectiveGenomeSize|effectiveGenomeSize": "2451960000", "scaling|effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "outFileFormat": "bedgraph", "advancedOpt|showAdvancedOpt": "no"}, "job": {"model_class": "Job", "id": "f4f3e423337ae3b0", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:06:53.044773", "create_time": "2024-08-30T13:06:42.315394", "galaxy_version": "23.1", "command_version": "bamCoverage 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "history_id": "156c4392fa643bca", "external_id": "gxy-sdgxl", "command_line": "ln -s '/galaxy/server/database/objects/d/f/f/dataset_dffaa440-2d02-4392-8f8e-421ef7cbe075.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/7/1/4/metadata_7146906b-6599-4fa2-b478-68f7f2c8e756.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/a/7/d/dataset_a7dc6700-a27c-4922-bf0e-c82c8a97e23c.dat' --outFileFormat 'bedgraph' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "region": "\"\"", "exactScaling": "false", "outFileFormat": "\"bedgraph\"", "scaling": "{\"__current_case__\": 4, \"effectiveGenomeSize\": {\"__current_case__\": 0, \"effectiveGenomeSize\": \"2451960000\", \"effectiveGenomeSize_opt\": \"specific\"}, \"type\": \"1x\"}", "binSize": "\"10\""}, "inputs": {"bamInput": {"id": "ba18cd8c087f0154", "src": "hda", "uuid": "dffaa440-2d02-4392-8f8e-421ef7cbe075"}}, "outputs": {"outFileName": {"id": "38e5943f3cf9e7a1", "src": "hda", "uuid": "a7dc6700-a27c-4922-bf0e-c82c8a97e23c"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 13:06:45", "plugin": "core", "name": "end_epoch", "raw_value": "1725023205.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:06:44", "plugin": "core", "name": "start_epoch", "raw_value": "1725023204.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-3", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 3, "time_seconds": 29.18935537338257, "inputs": {"bamInput": {"src": "hda", "id": "5835e2fe3b1be6c6"}, "binSize": "10", "scaling|effectiveGenomeSize|effectiveGenomeSize": "2451960000", "scaling|effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "outFileFormat": "bigwig", "advancedOpt|showAdvancedOpt": "no"}, "job": {"model_class": "Job", "id": "18cc197ba26e8e47", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:07:22.505998", "create_time": "2024-08-30T13:07:11.203374", "galaxy_version": "23.1", "command_version": "bamCoverage 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "history_id": "156c4392fa643bca", "external_id": "gxy-jbxxd", "command_line": "ln -s '/galaxy/server/database/objects/5/8/c/dataset_58c8ab4c-194d-40f6-8a4e-e1521e586719.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/2/c/3/metadata_2c358893-1e49-4d64-bc55-c4cccab338d5.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/f/0/6/dataset_f060a4c7-ff5a-4892-b273-51e1ee4e153a.dat' --outFileFormat 'bigwig' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "region": "\"\"", "exactScaling": "false", "outFileFormat": "\"bigwig\"", "scaling": "{\"__current_case__\": 4, \"effectiveGenomeSize\": {\"__current_case__\": 0, \"effectiveGenomeSize\": \"2451960000\", \"effectiveGenomeSize_opt\": \"specific\"}, \"type\": \"1x\"}", "binSize": "\"10\""}, "inputs": {"bamInput": {"id": "5835e2fe3b1be6c6", "src": "hda", "uuid": "58c8ab4c-194d-40f6-8a4e-e1521e586719"}}, "outputs": {"outFileName": {"id": "af686d0530be6436", "src": "hda", "uuid": "f060a4c7-ff5a-4892-b273-51e1ee4e153a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 13:07:13", "plugin": "core", "name": "end_epoch", "raw_value": "1725023233.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:07:12", "plugin": "core", "name": "start_epoch", "raw_value": "1725023232.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-4", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 4, "time_seconds": 27.349674701690674, "inputs": {"bamInput": {"src": "hda", "id": "ea3e808f13e0175c"}, "binSize": "10", "scaling|effectiveGenomeSize|effectiveGenomeSize": "2451960000", "scaling|effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "outFileFormat": "bedgraph", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "7a3a784002d9b2e4", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:07:49.918245", "create_time": "2024-08-30T13:07:39.202035", "galaxy_version": "23.1", "command_version": "bamCoverage 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "history_id": "156c4392fa643bca", "external_id": "gxy-cshkp", "command_line": "ln -s '/galaxy/server/database/objects/5/4/b/dataset_54b0d192-c778-471c-8242-7d1c2e3170a1.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/f/c/f/metadata_fcf7221d-eef9-45a6-a569-74221ec4cd00.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/8/4/3/dataset_843bde66-95bb-404e-8b4c-42447c462c0b.dat' --outFileFormat 'bedgraph' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000 --scaleFactor 1.0 --minMappingQuality '1'", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"MNase\": false, \"Offset\": \"\", \"__current_case__\": 1, \"blackListFileName\": null, \"centerReads\": false, \"doExtendCustom\": {\"__current_case__\": 0, \"doExtend\": \"no\"}, \"filterRNAstrand\": \"no\", \"ignoreDuplicates\": false, \"ignoreForNormalization\": \"\", \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"1\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"scaleFactor\": \"1.0\", \"showAdvancedOpt\": \"yes\", \"skipNAs\": false, \"smoothLength\": \"\"}", "region": "\"\"", "exactScaling": "false", "outFileFormat": "\"bedgraph\"", "scaling": "{\"__current_case__\": 4, \"effectiveGenomeSize\": {\"__current_case__\": 0, \"effectiveGenomeSize\": \"2451960000\", \"effectiveGenomeSize_opt\": \"specific\"}, \"type\": \"1x\"}", "binSize": "\"10\""}, "inputs": {"bamInput": {"id": "ea3e808f13e0175c", "src": "hda", "uuid": "54b0d192-c778-471c-8242-7d1c2e3170a1"}}, "outputs": {"outFileName": {"id": "69d3ae81c95d70aa", "src": "hda", "uuid": "843bde66-95bb-404e-8b4c-42447c462c0b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: 1\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: 1\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 13:07:41", "plugin": "core", "name": "end_epoch", "raw_value": "1725023261.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:07:40", "plugin": "core", "name": "start_epoch", "raw_value": "1725023260.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-5", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 5, "time_seconds": 28.361011028289795, "inputs": {"bamInput": {"src": "hda", "id": "64230aeb22c84d37"}, "binSize": "10", "scaling|effectiveGenomeSize|effectiveGenomeSize": "2451960000", "scaling|effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "outFileFormat": "bigwig", "advancedOpt|filterRNAstrand": "reverse", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "44901ea38dea194c", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:08:18.490621", "create_time": "2024-08-30T13:08:08.119631", "galaxy_version": "23.1", "command_version": "bamCoverage 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "history_id": "156c4392fa643bca", "external_id": "gxy-xnzxg", "command_line": "ln -s '/galaxy/server/database/objects/b/b/4/dataset_bb442541-d924-4bf9-9e47-2d1fb0c0be91.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/c/3/c/metadata_c3c939e3-98d0-4521-bada-4827a472be86.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/0/2/a/dataset_02a269e2-737e-4759-9f4f-b13347209855.dat' --outFileFormat 'bigwig' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000 --scaleFactor 1.0 --minMappingQuality '1' --filterRNAstrand 'reverse'", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"MNase\": false, \"Offset\": \"\", \"__current_case__\": 1, \"blackListFileName\": null, \"centerReads\": false, \"doExtendCustom\": {\"__current_case__\": 0, \"doExtend\": \"no\"}, \"filterRNAstrand\": \"reverse\", \"ignoreDuplicates\": false, \"ignoreForNormalization\": \"\", \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"1\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"scaleFactor\": \"1.0\", \"showAdvancedOpt\": \"yes\", \"skipNAs\": false, \"smoothLength\": \"\"}", "region": "\"\"", "exactScaling": "false", "outFileFormat": "\"bigwig\"", "scaling": "{\"__current_case__\": 4, \"effectiveGenomeSize\": {\"__current_case__\": 0, \"effectiveGenomeSize\": \"2451960000\", \"effectiveGenomeSize_opt\": \"specific\"}, \"type\": \"1x\"}", "binSize": "\"10\""}, "inputs": {"bamInput": {"id": "64230aeb22c84d37", "src": "hda", "uuid": "bb442541-d924-4bf9-9e47-2d1fb0c0be91"}}, "outputs": {"outFileName": {"id": "0a733565a2cc8703", "src": "hda", "uuid": "02a269e2-737e-4759-9f4f-b13347209855"}}, "output_collections": {}, "tool_stdout": "Due to filtering, 51.08108108108108% of the aforementioned alignments will be used 1115.6108108108108\n", "tool_stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: 1\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\nfilter_strand: reverse\nOffset: [1, -1]\n", "job_stdout": "", "job_stderr": "", "stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: 1\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\nfilter_strand: reverse\nOffset: [1, -1]\n", "stdout": "Due to filtering, 51.08108108108108% of the aforementioned alignments will be used 1115.6108108108108\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 13:08:10", "plugin": "core", "name": "end_epoch", "raw_value": "1725023290.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:08:09", "plugin": "core", "name": "start_epoch", "raw_value": "1725023289.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-6", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 6, "time_seconds": 29.422980785369873, "inputs": {"bamInput": {"src": "hda", "id": "46ab739d7abf1b46"}, "binSize": "10", "scaling|type": "no", "outFileFormat": "bigwig", "advancedOpt|doExtendCustom|doExtend": "yes", "advancedOpt|minMappingQuality": "0", "advancedOpt|Offset": "-4 -1", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "6e95eddc84cda40d", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:08:47.876456", "create_time": "2024-08-30T13:08:36.407755", "galaxy_version": "23.1", "command_version": "bamCoverage 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "history_id": "156c4392fa643bca", "external_id": "gxy-44zgc", "command_line": "ln -s '/galaxy/server/database/objects/a/2/6/dataset_a2663303-53a7-4851-8ea3-85c2e9c3e5a2.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/6/7/6/metadata_6767c2d4-35a1-4807-840b-9daba8b6e916.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/5/a/9/dataset_5a97ade3-b438-47da-bbcf-c0c0547642ed.dat' --outFileFormat 'bigwig' --binSize 10 --scaleFactor 1.0 --extendReads --Offset -4 -1", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"MNase\": false, \"Offset\": \"-4 -1\", \"__current_case__\": 1, \"blackListFileName\": null, \"centerReads\": false, \"doExtendCustom\": {\"__current_case__\": 1, \"doExtend\": \"yes\"}, \"filterRNAstrand\": \"no\", \"ignoreDuplicates\": false, \"ignoreForNormalization\": \"\", \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"0\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"scaleFactor\": \"1.0\", \"showAdvancedOpt\": \"yes\", \"skipNAs\": false, \"smoothLength\": \"\"}", "region": "\"\"", "exactScaling": "false", "outFileFormat": "\"bigwig\"", "scaling": "{\"__current_case__\": 3, \"type\": \"no\"}", "binSize": "\"10\""}, "inputs": {"bamInput": {"id": "46ab739d7abf1b46", "src": "hda", "uuid": "a2663303-53a7-4851-8ea3-85c2e9c3e5a2"}}, "outputs": {"outFileName": {"id": "dbc48d8df69af2d4", "src": "hda", "uuid": "5a97ade3-b438-47da-bbcf-c0c0547642ed"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "bamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: 242\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 968\nfilter_strand: None\nOffset: [-4, -1]\n", "job_stdout": "", "job_stderr": "", "stderr": "bamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: 242\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 968\nfilter_strand: None\nOffset: [-4, -1]\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 13:08:39", "plugin": "core", "name": "end_epoch", "raw_value": "1725023319.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:08:38", "plugin": "core", "name": "start_epoch", "raw_value": "1725023318.0000000"}, {"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_compute_matrix/3.3.2.0.0-0", "has_data": true, "data": {"tool_id": "deeptools_compute_matrix", "tool_version": "3.3.2.0.0", "test_index": 0, "time_seconds": 52.00021052360535, "inputs": {"regionsFiles_0|regionsFile": {"src": "hda", "id": "7cf1947c1168a2c0"}, "multibigwig_conditional|bigwigfiles": {"src": "hda", "id": "18cc197ba26e8e47"}, "mode|beforeRegionStartLength": "10", "mode|afterRegionStartLength": "10", "mode|mode_select": "reference-point", "advancedOpt|binSize": "10", "advancedOpt|sortUsing": "sum", "advancedOpt|averageTypeBins": "sum", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "b45576da8fb4db6c", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:04:23.330709", "create_time": "2024-08-30T13:03:50.569902", "galaxy_version": "23.1", "command_version": "computeMatrix 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0", "history_id": "156c4392fa643bca", "external_id": "gxy-75jnm", "command_line": "ln -f -s '/galaxy/server/database/objects/d/0/9/dataset_d091e297-9814-44d0-81f9-bde5eff59c9a.dat' 'bamCoverage_result4.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/3/6/a/dataset_36ad315c-c851-4298-9586-77480d086cb7.dat' 'computeMatrix1_bed_0.bed' && computeMatrix reference-point --regionsFileName 'computeMatrix1_bed_0.bed' --scoreFileName 'bamCoverage_result4.bw_0.bw' --outFileName '/galaxy/server/database/objects/9/4/d/dataset_94dca09d-bbee-4556-a511-a4b62e5e105b.dat' --samplesLabel 'bamCoverage_result4.bw' --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --referencePoint TSS --beforeRegionStartLength 10 --afterRegionStartLength 10 --sortRegions 'keep' --sortUsing 'sum' --averageTypeBins 'sum' --binSize 10 --transcriptID transcript --exonID exon --transcript_id_designator transcript_id", "traceback": null, "params": {"__input_ext": "\"bed\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 1, \"averageTypeBins\": \"sum\", \"binSize\": \"10\", \"blackListFileName\": null, \"exonID\": \"exon\", \"maxThreshold\": \"\", \"metagene\": false, \"minThreshold\": \"\", \"missingDataAsZero\": false, \"scale\": \"\", \"showAdvancedOpt\": \"yes\", \"skipZeros\": false, \"sortRegions\": \"keep\", \"sortUsing\": \"sum\", \"transcriptID\": \"transcript\", \"transcript_id_designator\": \"transcript_id\"}", "output": "{\"__current_case__\": 0, \"showOutputSettings\": \"no\"}", "mode": "{\"__current_case__\": 1, \"afterRegionStartLength\": \"10\", \"beforeRegionStartLength\": \"10\", \"mode_select\": \"reference-point\", \"nanAfterEnd\": false, \"referencePoint\": \"TSS\"}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibigwig_conditional": "{\"__current_case__\": 0, \"bigwigfiles\": {\"values\": [{\"id\": 78, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}", "regionsFiles": "[{\"__index__\": 0, \"regionsFile\": {\"values\": [{\"id\": 77, \"src\": \"hda\"}]}}]"}, "inputs": {"regionsFiles_0|regionsFile": {"id": "7cf1947c1168a2c0", "src": "hda", "uuid": "36ad315c-c851-4298-9586-77480d086cb7"}, "multibigwig_conditional|bigwigfiles1": {"id": "18cc197ba26e8e47", "src": "hda", "uuid": "d091e297-9814-44d0-81f9-bde5eff59c9a"}, "multibigwig_conditional|bigwigfiles": {"id": "18cc197ba26e8e47", "src": "hda", "uuid": "d091e297-9814-44d0-81f9-bde5eff59c9a"}}, "outputs": {"outFileName": {"id": "c20446b95cd50d61", "src": "hda", "uuid": "94dca09d-bbee-4556-a511-a4b62e5e105b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 13:04:08", "plugin": "core", "name": "end_epoch", "raw_value": "1725023048.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:04:07", "plugin": "core", "name": "start_epoch", "raw_value": "1725023047.0000000"}, {"title": "Memory Allocated (MB)", "value": "32212", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32212.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_compute_matrix/3.3.2.0.0-1", "has_data": true, "data": {"tool_id": "deeptools_compute_matrix", "tool_version": "3.3.2.0.0", "test_index": 1, "time_seconds": 30.816587448120117, "inputs": {"regionsFiles_0|regionsFile": {"src": "hda", "id": "7a3a784002d9b2e4"}, "multibigwig_conditional|bigwigfiles": {"src": "hda", "id": "0ff3cf4cdd53f073"}, "mode|beforeRegionStartLength": "10", "mode|afterRegionStartLength": "10", "mode|mode_select": "reference-point", "advancedOpt|binSize": "10", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "d9f9da59e3f2406f", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:04:54.369038", "create_time": "2024-08-30T13:04:41.646911", "galaxy_version": "23.1", "command_version": "computeMatrix 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0", "history_id": "156c4392fa643bca", "external_id": "gxy-6d98r", "command_line": "ln -f -s '/galaxy/server/database/objects/9/b/1/dataset_9b1ab5f4-4dca-43fe-a030-f321a3fdf0e4.dat' 'computeMatrix2.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/c/3/d/dataset_c3de79b2-2c5b-4f58-a4ec-959fb55be1c3.dat' 'computeMatrix2_bed_0.bed' && computeMatrix reference-point --regionsFileName 'computeMatrix2_bed_0.bed' --scoreFileName 'computeMatrix2.bw_0.bw' --outFileName '/galaxy/server/database/objects/b/c/b/dataset_bcb97d3c-b445-46b8-bd04-19e1e086f8a7.dat' --samplesLabel 'computeMatrix2.bw' --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --referencePoint TSS --beforeRegionStartLength 10 --afterRegionStartLength 10 --sortRegions 'keep' --sortUsing 'mean' --averageTypeBins 'mean' --binSize 10 --transcriptID transcript --exonID exon --transcript_id_designator transcript_id", "traceback": null, "params": {"__input_ext": "\"bed\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 1, \"averageTypeBins\": \"mean\", \"binSize\": \"10\", \"blackListFileName\": null, \"exonID\": \"exon\", \"maxThreshold\": \"\", \"metagene\": false, \"minThreshold\": \"\", \"missingDataAsZero\": false, \"scale\": \"\", \"showAdvancedOpt\": \"yes\", \"skipZeros\": false, \"sortRegions\": \"keep\", \"sortUsing\": \"mean\", \"transcriptID\": \"transcript\", \"transcript_id_designator\": \"transcript_id\"}", "output": "{\"__current_case__\": 0, \"showOutputSettings\": \"no\"}", "mode": "{\"__current_case__\": 1, \"afterRegionStartLength\": \"10\", \"beforeRegionStartLength\": \"10\", \"mode_select\": \"reference-point\", \"nanAfterEnd\": false, \"referencePoint\": \"TSS\"}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibigwig_conditional": "{\"__current_case__\": 0, \"bigwigfiles\": {\"values\": [{\"id\": 81, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}", "regionsFiles": "[{\"__index__\": 0, \"regionsFile\": {\"values\": [{\"id\": 80, \"src\": \"hda\"}]}}]"}, "inputs": {"multibigwig_conditional|bigwigfiles1": {"id": "0ff3cf4cdd53f073", "src": "hda", "uuid": "9b1ab5f4-4dca-43fe-a030-f321a3fdf0e4"}, "multibigwig_conditional|bigwigfiles": {"id": "0ff3cf4cdd53f073", "src": "hda", "uuid": "9b1ab5f4-4dca-43fe-a030-f321a3fdf0e4"}, "regionsFiles_0|regionsFile": {"id": "7a3a784002d9b2e4", "src": "hda", "uuid": "c3de79b2-2c5b-4f58-a4ec-959fb55be1c3"}}, "outputs": {"outFileName": {"id": "44901ea38dea194c", "src": "hda", "uuid": "bcb97d3c-b445-46b8-bd04-19e1e086f8a7"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 13:04:45", "plugin": "core", "name": "end_epoch", "raw_value": "1725023085.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:04:44", "plugin": "core", "name": "start_epoch", "raw_value": "1725023084.0000000"}, {"title": "Memory Allocated (MB)", "value": "32212", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32212.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_compute_matrix/3.3.2.0.0-2", "has_data": true, "data": {"tool_id": "deeptools_compute_matrix", "tool_version": "3.3.2.0.0", "test_index": 2, "time_seconds": 29.464679718017578, "inputs": {"regionsFiles_0|regionsFile": {"src": "hda", "id": "21383bfca5be1aac"}, "multibigwig_conditional|bigwigfiles": {"src": "hda", "id": "6e95eddc84cda40d"}, "mode|mode_select": "scale-regions", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "5ea0491d7d9d49ff", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:05:23.941401", "create_time": "2024-08-30T13:05:12.389170", "galaxy_version": "23.1", "command_version": "computeMatrix 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0", "history_id": "156c4392fa643bca", "external_id": "gxy-zlh2c", "command_line": "ln -f -s '/galaxy/server/database/objects/4/c/4/dataset_4c462518-cffb-40de-beef-22f00860aec2.dat' 'computeMatrix2.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/a/3/1/dataset_a3100f19-1c62-4980-9777-88d9c603ea51.dat' 'computeMatrix2_bed_0.bed' && computeMatrix scale-regions --regionsFileName 'computeMatrix2_bed_0.bed' --scoreFileName 'computeMatrix2.bw_0.bw' --outFileName '/galaxy/server/database/objects/f/5/d/dataset_f5d34cd0-fd0d-4cc8-b1e6-af2386f4a891.dat' --samplesLabel 'computeMatrix2.bw' --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --regionBodyLength 500 --sortRegions 'keep' --sortUsing 'mean' --averageTypeBins 'mean' --binSize 50 --transcriptID transcript --exonID exon --transcript_id_designator transcript_id", "traceback": null, "params": {"__input_ext": "\"bed\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 1, \"averageTypeBins\": \"mean\", \"binSize\": \"50\", \"blackListFileName\": null, \"exonID\": \"exon\", \"maxThreshold\": \"\", \"metagene\": false, \"minThreshold\": \"\", \"missingDataAsZero\": false, \"scale\": \"\", \"showAdvancedOpt\": \"yes\", \"skipZeros\": false, \"sortRegions\": \"keep\", \"sortUsing\": \"mean\", \"transcriptID\": \"transcript\", \"transcript_id_designator\": \"transcript_id\"}", "output": "{\"__current_case__\": 0, \"showOutputSettings\": \"no\"}", "mode": "{\"__current_case__\": 0, \"mode_select\": \"scale-regions\", \"regionBodyLength\": \"500\", \"regionStartLength\": {\"__current_case__\": 0, \"regionStartLength_select\": \"no\"}}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibigwig_conditional": "{\"__current_case__\": 0, \"bigwigfiles\": {\"values\": [{\"id\": 84, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}", "regionsFiles": "[{\"__index__\": 0, \"regionsFile\": {\"values\": [{\"id\": 83, \"src\": \"hda\"}]}}]"}, "inputs": {"regionsFiles_0|regionsFile": {"id": "21383bfca5be1aac", "src": "hda", "uuid": "a3100f19-1c62-4980-9777-88d9c603ea51"}, "multibigwig_conditional|bigwigfiles1": {"id": "6e95eddc84cda40d", "src": "hda", "uuid": "4c462518-cffb-40de-beef-22f00860aec2"}, "multibigwig_conditional|bigwigfiles": {"id": "6e95eddc84cda40d", "src": "hda", "uuid": "4c462518-cffb-40de-beef-22f00860aec2"}}, "outputs": {"outFileName": {"id": "6438f3d32c4013c9", "src": "hda", "uuid": "f5d34cd0-fd0d-4cc8-b1e6-af2386f4a891"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "A region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) ca8 ch3:75:100. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) cda8 ch3:100:125. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) ca5 ch2:125:150. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) cda5 ch2:150:175. Skipping...\n", "job_stdout": "", "job_stderr": "", "stderr": "A region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) ca8 ch3:75:100. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) cda8 ch3:100:125. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) ca5 ch2:125:150. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) cda5 ch2:150:175. Skipping...\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 13:05:15", "plugin": "core", "name": "end_epoch", "raw_value": "1725023115.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:05:14", "plugin": "core", "name": "start_epoch", "raw_value": "1725023114.0000000"}, {"title": "Memory Allocated (MB)", "value": "32212", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32212.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.73+galaxy0-0", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.73+galaxy0", "test_index": 0, "time_seconds": 43.515509605407715, "inputs": {"input_file": {"src": "hda", "id": "e297cd7ed0a5dd6c"}}, "job": {"model_class": "Job", "id": "9d1e1747721329c1", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:50:33.849702", "create_time": "2024-08-30T12:50:09.723398", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-tbnvt", "command_line": "ln -s '/galaxy/server/database/objects/c/0/5/dataset_c0587c6b-3b82-4cf3-906f-37b653c8b64d.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a_files' && fastqc --outdir '/galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a_files' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/9/1/a/dataset_91a6defe-bf0d-45b5-a4fd-61f548b6e00a_files'/*\\.html output.html", "traceback": null, "params": {"__input_ext": "\"fastqsanger\"", "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": "e297cd7ed0a5dd6c", "src": "hda", "uuid": "c0587c6b-3b82-4cf3-906f-37b653c8b64d"}}, "outputs": {"text_file": {"id": "4a8a894582b5f73d", "src": "hda", "uuid": "8d259d6e-686d-4fac-baf0-ccde3d91bf7c"}, "html_file": {"id": "9d1e1747721329c1", "src": "hda", "uuid": "91a6defe-bf0d-45b5-a4fd-61f548b6e00a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:50:21", "plugin": "core", "name": "end_epoch", "raw_value": "1725022221.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:50:19", "plugin": "core", "name": "start_epoch", "raw_value": "1725022219.0000000"}, {"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/0.73+galaxy0-1", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.73+galaxy0", "test_index": 1, "time_seconds": 32.78041481971741, "inputs": {"input_file": {"src": "hda", "id": "29c629bc39007a7f"}, "contaminants": {"src": "hda", "id": "15560a63e74f84d3"}}, "job": {"model_class": "Job", "id": "15560a63e74f84d3", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:51:06.699038", "create_time": "2024-08-30T12:50:53.682153", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-h5rcn", "command_line": "ln -s '/galaxy/server/database/objects/0/9/3/dataset_093bc3f7-a38d-426a-891b-8a0bf1b6135c.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e_files' && fastqc --outdir '/galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e_files' --contaminants '/galaxy/server/database/objects/b/3/c/dataset_b3ccb58b-38b9-4a18-afbd-b672e05d2ab2.dat' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/f/d/3/dataset_fd3796d9-54c8-4c39-be8c-20949645f10e_files'/*\\.html output.html", "traceback": null, "params": {"adapters": null, "limits": null, "nogroup": "false", "min_length": "\"\"", "kmers": "\"7\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger\""}, "inputs": {"contaminants": {"id": "15560a63e74f84d3", "src": "hda", "uuid": "b3ccb58b-38b9-4a18-afbd-b672e05d2ab2"}, "input_file": {"id": "29c629bc39007a7f", "src": "hda", "uuid": "093bc3f7-a38d-426a-891b-8a0bf1b6135c"}}, "outputs": {"text_file": {"id": "fa0229a69e711bff", "src": "hda", "uuid": "e6cff499-28ac-43d0-bfa3-44f0a321f171"}, "html_file": {"id": "6ac9981049d706dd", "src": "hda", "uuid": "fd3796d9-54c8-4c39-be8c-20949645f10e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:50:57", "plugin": "core", "name": "end_epoch", "raw_value": "1725022257.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:50:55", "plugin": "core", "name": "start_epoch", "raw_value": "1725022255.0000000"}, {"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/0.73+galaxy0-2", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.73+galaxy0", "test_index": 2, "time_seconds": 34.43050694465637, "inputs": {"input_file": {"src": "hda", "id": "c47be949479cc5b9"}, "adapters": {"src": "hda", "id": "d3f02b5a33fb39af"}}, "job": {"model_class": "Job", "id": "c47be949479cc5b9", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:51:41.260137", "create_time": "2024-08-30T12:51:27.916542", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-w5mjn", "command_line": "ln -s '/galaxy/server/database/objects/6/3/7/dataset_637bb09e-fd66-434a-a23a-20571bc3766e.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf_files' && fastqc --outdir '/galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf_files' --adapters '/galaxy/server/database/objects/2/5/5/dataset_25551fa7-9cbf-4974-b1e1-8caf0ab846b7.dat' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/7/6/4/dataset_7646ffa7-cb02-4b10-a714-463d3bd552bf_files'/*\\.html output.html", "traceback": null, "params": {"contaminants": null, "limits": null, "nogroup": "false", "min_length": "\"\"", "kmers": "\"7\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger\""}, "inputs": {"adapters": {"id": "d3f02b5a33fb39af", "src": "hda", "uuid": "25551fa7-9cbf-4974-b1e1-8caf0ab846b7"}, "input_file": {"id": "c47be949479cc5b9", "src": "hda", "uuid": "637bb09e-fd66-434a-a23a-20571bc3766e"}}, "outputs": {"text_file": {"id": "f740d3c7d43bd3eb", "src": "hda", "uuid": "9ac06e3f-d38f-4f89-95c1-056016abfd3e"}, "html_file": {"id": "080baf71aa6e2015", "src": "hda", "uuid": "7646ffa7-cb02-4b10-a714-463d3bd552bf"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:51:32", "plugin": "core", "name": "end_epoch", "raw_value": "1725022292.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:51:29", "plugin": "core", "name": "start_epoch", "raw_value": "1725022289.0000000"}, {"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/0.73+galaxy0-3", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.73+galaxy0", "test_index": 3, "time_seconds": 32.264431953430176, "inputs": {"input_file": {"src": "hda", "id": "a3a4551013810557"}, "limits": {"src": "hda", "id": "6acf2c47ca86c8b2"}}, "job": {"model_class": "Job", "id": "f740d3c7d43bd3eb", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:52:13.795741", "create_time": "2024-08-30T12:52:01.639806", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-xvcln", "command_line": "ln -s '/galaxy/server/database/objects/f/f/b/dataset_ffb6184f-a121-41b3-837c-8f3a099c9048.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a_files' && fastqc --outdir '/galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a_files' --limits '/galaxy/server/database/objects/c/e/b/dataset_ceb1cdac-974a-4475-a571-0208f86c0467.dat' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/7/c/5/dataset_7c535982-a2d2-44de-9be2-7b3bb6da281a_files'/*\\.html output.html", "traceback": null, "params": {"contaminants": null, "adapters": null, "nogroup": "false", "min_length": "\"\"", "kmers": "\"7\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger\""}, "inputs": {"input_file": {"id": "a3a4551013810557", "src": "hda", "uuid": "ffb6184f-a121-41b3-837c-8f3a099c9048"}, "limits": {"id": "6acf2c47ca86c8b2", "src": "hda", "uuid": "ceb1cdac-974a-4475-a571-0208f86c0467"}}, "outputs": {"html_file": {"id": "af40f508fdc35ec2", "src": "hda", "uuid": "7c535982-a2d2-44de-9be2-7b3bb6da281a"}, "text_file": {"id": "c97ee8434250db99", "src": "hda", "uuid": "983cc8d0-5f0b-4b1b-9496-40420a0f8288"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:52:03", "plugin": "core", "name": "start_epoch", "raw_value": "1725022323.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:52:05", "plugin": "core", "name": "end_epoch", "raw_value": "1725022325.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.73+galaxy0-4", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.73+galaxy0", "test_index": 4, "time_seconds": 33.626914262771606, "inputs": {"input_file": {"src": "hda", "id": "ee864d120e6ad4da"}, "limits": {"src": "hda", "id": "0fe7302a78654ddf"}, "kmers": "3"}, "job": {"model_class": "Job", "id": "af40f508fdc35ec2", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:52:47.401113", "create_time": "2024-08-30T12:52:34.877006", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-zpnw7", "command_line": "ln -s '/galaxy/server/database/objects/1/d/9/dataset_1d93d954-96ce-4797-b8e8-11b2549144ec.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7_files' && fastqc --outdir '/galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7_files' --limits '/galaxy/server/database/objects/3/5/d/dataset_35d5ef3b-89f7-4d65-add6-8b9bcf560943.dat' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 3 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/5/3/c/dataset_53c61e06-dcbb-4e7c-b446-de6e5d0042c7_files'/*\\.html output.html", "traceback": null, "params": {"contaminants": null, "adapters": null, "nogroup": "false", "min_length": "\"\"", "kmers": "\"3\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "ee864d120e6ad4da", "src": "hda", "uuid": "1d93d954-96ce-4797-b8e8-11b2549144ec"}, "limits": {"id": "0fe7302a78654ddf", "src": "hda", "uuid": "35d5ef3b-89f7-4d65-add6-8b9bcf560943"}}, "outputs": {"html_file": {"id": "d21247b92014bb0d", "src": "hda", "uuid": "53c61e06-dcbb-4e7c-b446-de6e5d0042c7"}, "text_file": {"id": "206b36d8f96e47cd", "src": "hda", "uuid": "c40250a1-d23d-4017-b352-0f1c9c7515d1"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:52:36", "plugin": "core", "name": "start_epoch", "raw_value": "1725022356.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:52:38", "plugin": "core", "name": "end_epoch", "raw_value": "1725022358.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.73+galaxy0-5", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.73+galaxy0", "test_index": 5, "time_seconds": 25.48966693878174, "inputs": {"input_file": {"src": "hda", "id": "8484cc763161da97"}, "min_length": "108"}, "job": {"model_class": "Job", "id": "ee864d120e6ad4da", "state": "error", "exit_code": null, "update_time": "2024-08-30T12:53:14.827157", "create_time": "2024-08-30T12:53:06.972295", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-lj7sk", "command_line": "ln -s '/galaxy/server/database/objects/c/7/7/dataset_c779310f-6c04-4ec2-a7b8-ed0679e21e17.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files' && fastqc --outdir '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files' --threads ${GALAXY_SLOTS:-2} --quiet --extract --min_length 108 --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/e/f/f/dataset_eff11dba-52dc-40a6-acb2-426075fb0264_files'/*\\.html output.html", "traceback": null, "params": {"contaminants": null, "adapters": null, "limits": null, "nogroup": "false", "min_length": "\"108\"", "kmers": "\"7\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger\""}, "inputs": {"input_file": {"id": "8484cc763161da97", "src": "hda", "uuid": "c779310f-6c04-4ec2-a7b8-ed0679e21e17"}}, "outputs": {"html_file": {"id": "3ca01b6fa3c2aaf5", "src": "hda", "uuid": "eff11dba-52dc-40a6-acb2-426075fb0264"}, "text_file": {"id": "633d64f77bff13b3", "src": "hda", "uuid": "366f2433-d768-44fa-bae1-205e2035b74c"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stderr": "", "stdout": "", "job_messages": null, "dependencies": [], "user_email": "tests@fake.org", "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "fastqc/0.73+galaxy0-6", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.73+galaxy0", "test_index": 6, "time_seconds": 33.38779950141907, "inputs": {"input_file": {"src": "hda", "id": "3976787d54723140"}, "nogroup": true}, "job": {"model_class": "Job", "id": "d21247b92014bb0d", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:53:46.567444", "create_time": "2024-08-30T12:53:32.242455", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-8v6cw", "command_line": "ln -s '/galaxy/server/database/objects/9/a/0/dataset_9a00d4ad-a9ba-44fc-8f09-8f4cb86209f3.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56_files' && fastqc --outdir '/galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56_files' --threads ${GALAXY_SLOTS:-2} --quiet --extract --nogroup --kmers 7 -f 'fastq' '1000trimmed_fastq' && cp '/galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/4/2/f/dataset_42fd57fd-513e-4678-a4d4-399e2da44b56_files'/*\\.html output.html", "traceback": null, "params": {"contaminants": null, "adapters": null, "limits": null, "nogroup": "true", "min_length": "\"\"", "kmers": "\"7\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "3976787d54723140", "src": "hda", "uuid": "9a00d4ad-a9ba-44fc-8f09-8f4cb86209f3"}}, "outputs": {"html_file": {"id": "6cded8ba9046fcf8", "src": "hda", "uuid": "42fd57fd-513e-4678-a4d4-399e2da44b56"}, "text_file": {"id": "106d1733a57037d1", "src": "hda", "uuid": "39a59496-43e8-4d2c-bf1e-4d87eea99427"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:53:34", "plugin": "core", "name": "start_epoch", "raw_value": "1725022414.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:53:37", "plugin": "core", "name": "end_epoch", "raw_value": "1725022417.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}]}, "status": "success"}}, {"id": "fastqc/0.73+galaxy0-7", "has_data": true, "data": {"tool_id": "fastqc", "tool_version": "0.73+galaxy0", "test_index": 7, "time_seconds": 32.354315519332886, "inputs": {"input_file": {"src": "hda", "id": "1ba62846d1f04d18"}}, "job": {"model_class": "Job", "id": "8484cc763161da97", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:54:18.941729", "create_time": "2024-08-30T12:54:05.474250", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-5zxm2", "command_line": "ln -s '/galaxy/server/database/objects/c/2/d/dataset_c2d9e4d7-8245-4adf-8f54-48436964c052.dat' 'hisat_output_1_bam' && mkdir -p '/galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b_files' && fastqc --outdir '/galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b_files' --threads ${GALAXY_SLOTS:-2} --quiet --extract --kmers 7 -f 'bam' 'hisat_output_1_bam' && cp '/galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/6/9/2/dataset_692e93d5-b8d6-4ead-b42a-696dd82e5c4b_files'/*\\.html output.html", "traceback": null, "params": {"contaminants": null, "adapters": null, "limits": null, "nogroup": "false", "min_length": "\"\"", "kmers": "\"7\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"input_file": {"id": "1ba62846d1f04d18", "src": "hda", "uuid": "c2d9e4d7-8245-4adf-8f54-48436964c052"}}, "outputs": {"html_file": {"id": "9df085a5453dfde2", "src": "hda", "uuid": "692e93d5-b8d6-4ead-b42a-696dd82e5c4b"}, "text_file": {"id": "54f87b52c320e6bc", "src": "hda", "uuid": "8223b98e-a5af-4f6b-be17-f355070397a5"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:54:07", "plugin": "core", "name": "start_epoch", "raw_value": "1725022447.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:54:09", "plugin": "core", "name": "end_epoch", "raw_value": "1725022449.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "lofreq_indelqual/2.1.5+galaxy0-0", "has_data": true, "data": {"tool_id": "lofreq_indelqual", "tool_version": "2.1.5+galaxy0", "test_index": 0, "time_seconds": 35.16563105583191, "inputs": {"reads": {"src": "hda", "id": "3b0653aec9b3bc8a"}, "strategy|insertions": "20", "strategy|deletions": "30", "strategy|selector": "uniform"}, "job": {"model_class": "Job", "id": "a570955de08d43f9", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:09:24.562907", "create_time": "2024-08-30T13:09:07.825673", "galaxy_version": "23.1", "command_version": "2.1.5", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-gkz7p", "command_line": "lofreq indelqual --uniform 20,30 -o output.bam /galaxy/server/database/objects/d/3/7/dataset_d37def15-5a08-4f52-acce-7e74389bb375.dat", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strategy": "{\"__current_case__\": 0, \"deletions\": \"30\", \"insertions\": \"20\", \"selector\": \"uniform\"}"}, "inputs": {"reads": {"id": "3b0653aec9b3bc8a", "src": "hda", "uuid": "d37def15-5a08-4f52-acce-7e74389bb375"}}, "outputs": {"output": {"id": "7c7bf5da8184cf66", "src": "hda", "uuid": "53373daf-3405-4d26-a409-3ced0d6ca9b0"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 13:09:13", "plugin": "core", "name": "end_epoch", "raw_value": "1725023353.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:09:13", "plugin": "core", "name": "start_epoch", "raw_value": "1725023353.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: different than expected, difference (using diff):\n( /tmp/tmpxv64f6yiindelqual-out1.bam v. /tmp/tmp6jgaw7qeindelqual-out1.bam )\nBinary data detected, not displaying diff"], "status": "failure"}}, {"id": "lofreq_indelqual/2.1.5+galaxy0-1", "has_data": true, "data": {"tool_id": "lofreq_indelqual", "tool_version": "2.1.5+galaxy0", "test_index": 1, "time_seconds": 29.271262407302856, "inputs": {"reads": {"src": "hda", "id": "912d335786d9cf15"}, "strategy|reference_source|ref": {"src": "hda", "id": "bd19e4f44660822b"}, "strategy|reference_source|ref_selector": "history", "strategy|selector": "dindel"}, "job": {"model_class": "Job", "id": "915a352ef8644fda", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:09:54.134190", "create_time": "2024-08-30T13:09:43.620515", "galaxy_version": "23.1", "command_version": "2.1.5", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-qvgr8", "command_line": "ln -s '/galaxy/server/database/objects/6/5/e/dataset_65e87b57-8d6e-429c-a56f-a894d04b1466.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && lofreq indelqual --dindel --ref reference.fa -o output.bam /galaxy/server/database/objects/d/5/5/dataset_d55d6a7e-3840-4d50-bd60-5c59e885f84c.dat", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strategy": "{\"__current_case__\": 1, \"reference_source\": {\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 103, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}, \"selector\": \"dindel\"}"}, "inputs": {"reads": {"id": "912d335786d9cf15", "src": "hda", "uuid": "d55d6a7e-3840-4d50-bd60-5c59e885f84c"}, "strategy|reference_source|ref": {"id": "bd19e4f44660822b", "src": "hda", "uuid": "65e87b57-8d6e-429c-a56f-a894d04b1466"}}, "outputs": {"output": {"id": "bfd974970f567736", "src": "hda", "uuid": "5edcb442-8f71-48fc-bf93-9638eee48f40"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 13:09:45", "plugin": "core", "name": "end_epoch", "raw_value": "1725023385.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:09:45", "plugin": "core", "name": "start_epoch", "raw_value": "1725023385.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: different than expected, difference (using diff):\n( /tmp/tmp4xjzy22yindelqual-out2.bam v. /tmp/tmpodw0kbjkindelqual-out2.bam )\nBinary data detected, not displaying diff"], "status": "failure"}}, {"id": "lofreq_indelqual/2.1.5+galaxy0-2", "has_data": true, "data": {"tool_id": "lofreq_indelqual", "tool_version": "2.1.5+galaxy0", "test_index": 2, "time_seconds": 28.099361896514893, "inputs": {"reads": {"src": "hda", "id": "3d8adfd73b24ffb7"}, "strategy|insertions": "20", "strategy|selector": "uniform"}, "job": {"model_class": "Job", "id": "38e5943f3cf9e7a1", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:10:22.437086", "create_time": "2024-08-30T13:10:11.487844", "galaxy_version": "23.1", "command_version": "2.1.5", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-7gbzv", "command_line": "lofreq indelqual --uniform 20 -o output.bam /galaxy/server/database/objects/5/9/4/dataset_594ed40a-fa19-42e9-b639-06d673bd3371.dat", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strategy": "{\"__current_case__\": 0, \"deletions\": \"\", \"insertions\": \"20\", \"selector\": \"uniform\"}"}, "inputs": {"reads": {"id": "3d8adfd73b24ffb7", "src": "hda", "uuid": "594ed40a-fa19-42e9-b639-06d673bd3371"}}, "outputs": {"output": {"id": "fe4a9a9ff8ecf50e", "src": "hda", "uuid": "c8483965-c12d-4b4c-8cf9-4194655849bb"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 13:10:13", "plugin": "core", "name": "end_epoch", "raw_value": "1725023413.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:10:13", "plugin": "core", "name": "start_epoch", "raw_value": "1725023413.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: different than expected, difference (using diff):\n( /tmp/tmpf2ixwdd_indelqual-out3.bam v. /tmp/tmp12njajikindelqual-out3.bam )\nBinary data detected, not displaying diff"], "status": "failure"}}, {"id": "mummer_nucmer/4.0.0beta2+galaxy1-0", "has_data": true, "data": {"tool_id": "mummer_nucmer", "tool_version": "4.0.0beta2+galaxy1", "test_index": 0, "time_seconds": 52.032447814941406, "inputs": {"reference_sequence": {"src": "hda", "id": "42d51d950cc8b6fa"}, "query_sequence": {"src": "hda", "id": "ef43737016b6b07b"}, "options|advanced": "defaults", "mumplot|sequences|seq_input": "yes", "mumplot|plot": "yes"}, "job": {"model_class": "Job", "id": "ea3e808f13e0175c", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:11:15.526788", "create_time": "2024-08-30T13:10:42.652521", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1", "history_id": "156c4392fa643bca", "external_id": "gxy-27j6x", "command_line": "ln -s /galaxy/server/database/objects/c/d/6/dataset_cd62bc4b-20da-4331-9648-812a1ad14831.dat reference.fa && ln -s /galaxy/server/database/objects/0/1/8/dataset_0189faf6-5079-43dd-a304-9b2ca6d3728d.dat query.fa && nucmer -b '200' -c '65' -D '5' -d '0.12' -g '90' -l '20' -L '0' --threads \"${GALAXY_SLOTS:-1}\" 'reference.fa' 'query.fa' && mummerplot -R '/galaxy/server/database/objects/c/d/6/dataset_cd62bc4b-20da-4331-9648-812a1ad14831.dat' -Q '/galaxy/server/database/objects/0/1/8/dataset_0189faf6-5079-43dd-a304-9b2ca6d3728d.dat' -b '20' -s 'small' -terminal png -title 'Title' 'out.delta' && gnuplot < out.gp", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "mumplot": "{\"__current_case__\": 0, \"breaklen\": \"20\", \"color\": \"\", \"coverage\": \"\", \"fat\": false, \"filter\": false, \"labels\": {\"IDs\": \"no\", \"__current_case__\": 1}, \"plot\": \"yes\", \"range\": {\"__current_case__\": 1, \"custom\": \"no\"}, \"sequences\": {\"__current_case__\": 0, \"layout\": false, \"query_sequence\": {\"values\": [{\"id\": 108, \"src\": \"hda\"}]}, \"reference_sequence\": {\"values\": [{\"id\": 108, \"src\": \"hda\"}]}, \"seq_input\": \"yes\"}, \"size\": \"small\", \"snp\": false, \"title\": \"Title\"}", "options": "{\"__current_case__\": 1, \"advanced\": \"defaults\"}", "nosimplify": "false", "nooptimize": "false", "minalign": "\"0\"", "minmatch": "\"20\"", "maxgap": "\"90\"", "direction": "\"\"", "noextend": "false", "diagfactor": "\"0.12\"", "diagdiff": "\"5\"", "mincluster": "\"65\"", "breaklen": "\"200\"", "anchoring": "\"\""}, "inputs": {"reference_sequence": {"id": "42d51d950cc8b6fa", "src": "hda", "uuid": "cd62bc4b-20da-4331-9648-812a1ad14831"}, "query_sequence": {"id": "ef43737016b6b07b", "src": "hda", "uuid": "0189faf6-5079-43dd-a304-9b2ca6d3728d"}, "mumplot|sequences|reference_sequence": {"id": "ef43737016b6b07b", "src": "hda", "uuid": "0189faf6-5079-43dd-a304-9b2ca6d3728d"}, "mumplot|sequences|query_sequence": {"id": "ef43737016b6b07b", "src": "hda", "uuid": "0189faf6-5079-43dd-a304-9b2ca6d3728d"}, "mumplot|sequences|query_sequence1": {"id": "ef43737016b6b07b", "src": "hda", "uuid": "0189faf6-5079-43dd-a304-9b2ca6d3728d"}}, "outputs": {"png_output": {"id": "4c3a1dcddd93b899", "src": "hda", "uuid": "09ff0a69-0d0b-4066-961a-2b1af50055f8"}, "delta_output": {"id": "6c618f6bcb06b8cc", "src": "hda", "uuid": "e7826b1d-ffbd-482b-bf3c-b70b8f7a2288"}}, "output_collections": {}, "tool_stdout": "gnuplot 5.2 patchlevel 7\n", "tool_stderr": "Reading delta file out.delta\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n", "job_stdout": "", "job_stderr": "", "stderr": "Reading delta file out.delta\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n", "stdout": "gnuplot 5.2 patchlevel 7\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 13:11:00", "plugin": "core", "name": "end_epoch", "raw_value": "1725023460.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:10:59", "plugin": "core", "name": "start_epoch", "raw_value": "1725023459.0000000"}, {"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": "poretools_hist/0.6.1a1.1-0", "has_data": true, "data": {"tool_id": "poretools_hist", "tool_version": "0.6.1a1.1", "test_index": 0, "time_seconds": 52.68317151069641, "inputs": {"input": {"src": "hda", "id": "b3563ccd5e1e3ab8"}, "extension": "png"}, "job": {"model_class": "Job", "id": "d0f64fa7dfce59dc", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:02:35.193392", "create_time": "2024-08-30T13:02:01.116792", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1", "history_id": "156c4392fa643bca", "external_id": "gxy-tlcgt", "command_line": "export MPLBACKEND=\"agg\" && poretools hist '/galaxy/server/database/objects/a/4/7/dataset_a473f856-9874-432a-af38-cb4c9b776d2b.dat' --saveas histogram.png --min-length 0 --max-length 1000000000 --num-bins 50 && mv histogram.png '/galaxy/server/database/objects/3/9/4/dataset_3945699f-1e5b-4f38-8b2b-37f4ac938d4c.dat'", "traceback": 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": "\"png\""}, "inputs": {"input": {"id": "b3563ccd5e1e3ab8", "src": "hda", "uuid": "a473f856-9874-432a-af38-cb4c9b776d2b"}}, "outputs": {"output": {"id": "e0b49637d014491c", "src": "hda", "uuid": "3945699f-1e5b-4f38-8b2b-37f4ac938d4c"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": 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"23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1", "history_id": "156c4392fa643bca", "external_id": "gxy-d28r2", "command_line": "export MPLBACKEND=\"agg\" && poretools hist '/galaxy/server/database/objects/3/1/4/dataset_31467151-7d33-4d0c-a100-9ed18f2b85be.dat' --saveas histogram.pdf --min-length 0 --max-length 1000000000 --num-bins 50 && mv histogram.pdf '/galaxy/server/database/objects/9/1/0/dataset_910b08e1-40f5-45eb-90a8-f77f403c3c73.dat'", "traceback": 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": "fbbbf1f96f8e5488", "src": "hda", "uuid": "31467151-7d33-4d0c-a100-9ed18f2b85be"}}, "outputs": {"output": {"id": "51e554051ef9c10a", "src": "hda", 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"samtools_markdup/1.9+galaxy2-0", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 0, "time_seconds": 28.86023211479187, "inputs": {"bamfile": {"src": "hda", "id": "7c01c4141514aa61"}}, "job": {"model_class": "Job", "id": "633d64f77bff13b3", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:54:51.300553", "create_time": "2024-08-30T12:54:38.840361", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "history_id": "156c4392fa643bca", "external_id": "gxy-2wpm7", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/c/7/7/dataset_c77f6a48-f5f4-4df1-b6bc-0a0bc393c562.dat' && samtools markdup -@ $addthreads coordsort.sam '/galaxy/server/database/objects/4/6/c/dataset_46c868b5-8a19-4133-9b9e-3b7292714b5e.dat'", "traceback": null, "params": {"remove": "false", "maxlen": "\"\"", "stats": "false", "supp": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"sam\""}, "inputs": {"bamfile": {"id": "7c01c4141514aa61", "src": "hda", "uuid": "c77f6a48-f5f4-4df1-b6bc-0a0bc393c562"}}, "outputs": {"output": {"id": "38e0158e5ebfa1e2", "src": "hda", "uuid": "46c868b5-8a19-4133-9b9e-3b7292714b5e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:54:42", "plugin": "core", "name": "start_epoch", "raw_value": "1725022482.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:54:42", "plugin": "core", "name": "end_epoch", "raw_value": "1725022482.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "output_problems": ["Output output: Test output file (5_markdup.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_markdup/1.9+galaxy2-1", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 1, "time_seconds": 21.81886625289917, "inputs": {"bamfile": {"src": "hda", "id": "0f3b0b88fd8d3bd3"}, "remove": true}, "job": {"model_class": "Job", "id": "6cded8ba9046fcf8", "state": "error", "exit_code": null, "update_time": "2024-08-30T12:55:13.131201", "create_time": "2024-08-30T12:55:08.534034", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "history_id": "156c4392fa643bca", "external_id": "gxy-f6mb4", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/9/8/8/dataset_988d51bd-daba-4ed9-a392-1ed7724aba4d.dat' && samtools markdup -@ $addthreads -r coordsort.sam '/galaxy/server/database/objects/a/6/6/dataset_a667be73-c02a-41a2-89f1-4bda7a51270c.dat'", "traceback": null, "params": {"remove": "true", "maxlen": "\"\"", "stats": "false", "supp": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"sam\""}, "inputs": {"bamfile": {"id": "0f3b0b88fd8d3bd3", "src": "hda", "uuid": "988d51bd-daba-4ed9-a392-1ed7724aba4d"}}, "outputs": {"output": {"id": "0a2d17a5e5658f2e", "src": "hda", "uuid": "a667be73-c02a-41a2-89f1-4bda7a51270c"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stderr": "", "stdout": "", "job_messages": null, "dependencies": [], "user_email": "tests@fake.org", "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "samtools_markdup/1.9+galaxy2-2", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 2, "time_seconds": 27.401360750198364, "inputs": {"bamfile": {"src": "hda", "id": "7eb12407ceab9b32"}, "supp": true}, "job": {"model_class": "Job", "id": "1ba62846d1f04d18", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:55:40.830322", "create_time": "2024-08-30T12:55:30.054890", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "history_id": "156c4392fa643bca", "external_id": "gxy-spz6r", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/e/3/d/dataset_e3dd87f7-3c64-473c-8c3a-9c905ae7adc5.dat' coordsort.sam && samtools markdup -@ $addthreads -S coordsort.sam '/galaxy/server/database/objects/1/5/1/dataset_15131c50-2549-4208-92bb-1aba16423f02.dat'", "traceback": null, "params": {"remove": "false", "maxlen": "\"\"", "stats": "false", "supp": "true", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"bamfile": {"id": "7eb12407ceab9b32", "src": "hda", "uuid": "e3dd87f7-3c64-473c-8c3a-9c905ae7adc5"}}, "outputs": {"output": {"id": "9de808f54edb8972", "src": "hda", "uuid": "15131c50-2549-4208-92bb-1aba16423f02"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:55:32", "plugin": "core", "name": "start_epoch", "raw_value": "1725022532.0000000"}, {"title": "Job End Time", "value": "2024-08-30 12:55:32", "plugin": "core", "name": "end_epoch", "raw_value": "1725022532.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "output_problems": ["Output output: Test output file (7_mark_supp_dup.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_markdup/1.9+galaxy2-3", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 3, "time_seconds": 27.91552186012268, "inputs": {"bamfile": {"src": "hda", "id": "408382c4a5d7521c"}, "stats": true}, "job": {"model_class": "Job", "id": "54f87b52c320e6bc", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:56:08.243765", "create_time": "2024-08-30T12:55:57.207189", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "history_id": "156c4392fa643bca", "external_id": "gxy-xsrkb", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/7/4/4/dataset_7449b6ab-4847-4f4a-8ddb-9a2571745d7e.dat' && samtools markdup -@ $addthreads -s coordsort.sam '/galaxy/server/database/objects/a/0/e/dataset_a0ebcb53-0ac7-46ae-aa45-b18cf80d2005.dat' 2> '/galaxy/server/database/objects/2/f/f/dataset_2ffa50c5-3185-42eb-9a0f-4c908879a988.dat'", "traceback": null, "params": {"remove": "false", "maxlen": "\"\"", "stats": "true", "supp": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"sam\""}, "inputs": {"bamfile": {"id": "408382c4a5d7521c", "src": "hda", "uuid": "7449b6ab-4847-4f4a-8ddb-9a2571745d7e"}}, "outputs": {"output": {"id": "019b97a522616e6d", "src": "hda", "uuid": "a0ebcb53-0ac7-46ae-aa45-b18cf80d2005"}, "stats_output": {"id": "81705c8bdfb2f0c3", "src": "hda", "uuid": "2ffa50c5-3185-42eb-9a0f-4c908879a988"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 12:55:59", "plugin": "core", "name": "end_epoch", "raw_value": "1725022559.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:55:59", "plugin": "core", "name": "start_epoch", "raw_value": "1725022559.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: Test output file (5_markdup.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it.", "Output stats_output: different than expected, difference (using diff):\n( /tmp/tmpdn6o4ht3stats.txt v. /tmp/tmpsabt06ecstats.txt )\n--- local_file\n+++ history_data\n@@ -1,16 +1,5 @@\n-COMMAND: samtools markdup -@ 0 -s coordsort.sam /tmp/tmpea8lprdd/files/2/2/4/dataset_224df993-f6bf-4c7d-99a1-2e9dd51c2a57.dat\n-READ: 16\n-WRITTEN: 16\n-EXCLUDED: 3\n-EXAMINED: 13\n-PAIRED: 10\n-SINGLE: 3\n-DUPLICATE PAIR: 4\n-DUPLICATE SINGLE: 2\n-DUPLICATE PAIR OPTICAL: 0\n-DUPLICATE SINGLE OPTICAL: 0\n-DUPLICATE NON PRIMARY: 0\n-DUPLICATE NON PRIMARY OPTICAL: 0\n-DUPLICATE PRIMARY TOTAL: 6\n-DUPLICATE TOTAL: 6\n-ESTIMATED_LIBRARY_SIZE: 4\n+READ 16 WRITTEN 16 \n+EXCLUDED 3 EXAMINED 13\n+PAIRED 10 SINGLE 3\n+DULPICATE PAIR 4 DUPLICATE SINGLE 2\n+DUPLICATE TOTAL 6\n"], "status": "failure"}}, {"id": "sqlite_to_tabular/2.0.1-0", "has_data": true, "data": {"tool_id": "sqlite_to_tabular", "tool_version": "2.0.1", "test_index": 0, "time_seconds": 67.74753308296204, "inputs": {"sqlitedb": {"src": "hda", "id": "156c4392fa643bca"}, "sqlquery": "SELECT first_name, last_name, age FROM contacts WHERE first_name = 'Sam'"}, "job": {"model_class": "Job", "id": "5dfc3409608a2061", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T12:49:50.092198", "create_time": "2024-08-30T12:49:11.259997", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1", "history_id": "156c4392fa643bca", "external_id": "gxy-j6bzm", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/bce29ec10b78/sqlite_to_tabular/sqlite_to_tabular.py' --sqlitedb='/galaxy/server/database/objects/8/f/5/dataset_8f5e1da9-3cda-44a5-b232-ed8c7392632c.dat' --query_file='/galaxy/server/database/jobs_directory/000/2/configs/tmp1yved69q' --comment_char='#' --output='/galaxy/server/database/objects/2/3/5/dataset_23577869-cd1d-401b-b4ee-5aa263810431.dat'", "traceback": null, "params": {"__input_ext": "\"sqlite\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT first_name, last_name, age FROM contacts WHERE first_name = 'Sam'\""}, "inputs": {"sqlitedb": {"id": "156c4392fa643bca", "src": "hda", "uuid": "8f5e1da9-3cda-44a5-b232-ed8c7392632c"}}, "outputs": {"query_results": {"id": "5dfc3409608a2061", "src": "hda", "uuid": "23577869-cd1d-401b-b4ee-5aa263810431"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 12:49:39", "plugin": "core", "name": "end_epoch", "raw_value": "1725022179.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:49:39", "plugin": "core", "name": "start_epoch", "raw_value": "1725022179.0000000"}, {"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": "vcfbedintersect/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfbedintersect", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 34.59898638725281, "inputs": {"vcf_input": {"src": "hda", "id": "b5fd60f450fc55cd"}, "bed_vs_interval|bed_input": {"src": "hda", "id": "4ed862dd399223fe"}, "bed_vs_interval|bed_vs_interval_selector": "bed", "invert": false}, "job": {"model_class": "Job", "id": "3a9d800057b68c29", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:00:08.445532", "create_time": "2024-08-30T12:59:52.344968", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-f768q", "command_line": "vcfintersect -b '/galaxy/server/database/objects/c/0/c/dataset_c0cb62bc-d241-470a-92c2-09bf6e325b65.dat' '/galaxy/server/database/objects/a/6/f/dataset_a6f72704-c648-4565-a679-1824a5039d9c.dat' > '/galaxy/server/database/objects/5/1/7/dataset_5171451e-a406-43d5-ad38-f8630cf9bd2d.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "invert": "false", "bed_vs_interval": "{\"__current_case__\": 0, \"bed_input\": {\"values\": [{\"id\": 59, \"src\": \"hda\"}]}, \"bed_vs_interval_selector\": \"bed\"}"}, "inputs": {"bed_vs_interval|bed_input": {"id": "4ed862dd399223fe", "src": "hda", "uuid": "c0cb62bc-d241-470a-92c2-09bf6e325b65"}, "vcf_input": {"id": "b5fd60f450fc55cd", "src": "hda", "uuid": "a6f72704-c648-4565-a679-1824a5039d9c"}}, "outputs": {"out_file1": {"id": "e91c490c9f6a73a2", "src": "hda", "uuid": "5171451e-a406-43d5-ad38-f8630cf9bd2d"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 12:59:58", "plugin": "core", "name": "end_epoch", "raw_value": "1725022798.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 12:59:58", "plugin": "core", "name": "start_epoch", "raw_value": "1725022798.0000000"}, {"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": "vcfbedintersect/1.0.0_rc3+galaxy0-1", "has_data": true, "data": {"tool_id": "vcfbedintersect", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 1, "time_seconds": 27.946234226226807, "inputs": {"vcf_input": {"src": "hda", "id": "95658726ede0b433"}, "bed_vs_interval|int_input": "20:1-30000", "bed_vs_interval|bed_vs_interval_selector": "interval", "invert": false}, "job": {"model_class": "Job", "id": "849d1de06f90547b", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:00:36.669750", "create_time": "2024-08-30T13:00:26.124038", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-z84ks", "command_line": "vcfintersect -R '20:1-30000' '/galaxy/server/database/objects/d/2/3/dataset_d2340288-58bf-408b-bf0f-14d66a7eaa8f.dat' > '/galaxy/server/database/objects/8/8/a/dataset_88a227fe-e761-4aab-9de1-8ee984b95784.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "invert": "false", "bed_vs_interval": "{\"__current_case__\": 1, \"bed_vs_interval_selector\": \"interval\", \"int_input\": \"20:1-30000\"}"}, "inputs": {"vcf_input": {"id": "95658726ede0b433", "src": "hda", "uuid": "d2340288-58bf-408b-bf0f-14d66a7eaa8f"}}, "outputs": {"out_file1": {"id": "fcf89f603a1c7b2a", "src": "hda", "uuid": "88a227fe-e761-4aab-9de1-8ee984b95784"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 13:00:28", "plugin": "core", "name": "end_epoch", "raw_value": "1725022828.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:00:28", "plugin": "core", "name": "start_epoch", "raw_value": "1725022828.0000000"}, {"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": "vcfvcfintersect/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfvcfintersect", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 32.517826080322266, "inputs": {"vcf_input1": {"src": "hda", "id": "f2e6b52237639f74"}, "vcf_input2": {"src": "hda", "id": "b45576da8fb4db6c"}, "reference_source|ref_file": {"src": "hda", "id": "513a309e28516acc"}, "reference_source|reference_source_selector": "history", "isect_union": "-i", "invert": false, "window_size": "30", "loci": false, "adv_options|adv_options_selector": "no"}, "job": {"model_class": "Job", "id": "ecde87cc004b1c6a", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:01:10.534811", "create_time": "2024-08-30T13:00:59.478660", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0", "history_id": "156c4392fa643bca", "external_id": "gxy-5gp7j", "command_line": "ln -s '/galaxy/server/database/objects/9/2/7/dataset_9272632b-1675-4e45-bd91-d5af269cd9b0.dat' 'localref.fa' && vcfintersect -r 'localref.fa' -w \"30\" -i '/galaxy/server/database/objects/d/3/a/dataset_d3a34ff3-1282-413a-ac33-853dc82f65a5.dat' '/galaxy/server/database/objects/1/9/4/dataset_194c884f-2c23-4f23-9110-28dfeeb81ea5.dat' > '/galaxy/server/database/objects/8/0/3/dataset_803ffafe-159b-4252-9e8a-4826ed1772b1.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv_options": "{\"__current_case__\": 0, \"adv_options_selector\": \"no\"}", "loci": "false", "window_size": "\"30\"", "invert": "false", "isect_union": "\"-i\"", "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 65, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"vcf_input1": {"id": "f2e6b52237639f74", "src": "hda", "uuid": "d3a34ff3-1282-413a-ac33-853dc82f65a5"}, "vcf_input2": {"id": "b45576da8fb4db6c", "src": "hda", "uuid": "194c884f-2c23-4f23-9110-28dfeeb81ea5"}, "reference_source|ref_file": {"id": "513a309e28516acc", "src": "hda", "uuid": "9272632b-1675-4e45-bd91-d5af269cd9b0"}}, "outputs": {"out_file1": {"id": "b21d89599c6459c7", "src": "hda", "uuid": "803ffafe-159b-4252-9e8a-4826ed1772b1"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "index file localref.fa.fai not found, generating...\n", "job_stdout": "", "job_stderr": "", "stderr": "index file localref.fa.fai not found, generating...\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 13:01:01", "plugin": "core", "name": "end_epoch", "raw_value": "1725022861.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 13:01:01", "plugin": "core", "name": "start_epoch", "raw_value": "1725022861.0000000"}, {"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": "vcfvcfintersect/1.0.0_rc3+galaxy0-1", "has_data": true, "data": {"tool_id": "vcfvcfintersect", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 1, "time_seconds": 30.849597930908203, "inputs": {"vcf_input1": {"src": "hda", "id": "d9f9da59e3f2406f"}, "vcf_input2": {"src": "hda", "id": "85c44b3c6b9e7586"}, "reference_source|ref_file": {"src": "hda", "id": "b9dde3d46c4379df"}, "reference_source|reference_source_selector": "history", "isect_union": "-u", "invert": false, "window_size": "30", "loci": false, "adv_options|adv_options_selector": "no"}, "job": {"model_class": "Job", "id": "e0569ebde28ee8e6", "state": "ok", "exit_code": 0, "update_time": "2024-08-30T13:01:41.362039", "create_time": "2024-08-30T13:01:31.371454", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": 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