From 665ad9bf32245505c97896a1e3ce3de395a6b726 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 24 Oct 2023 15:26:16 +0000 Subject: [PATCH] Updating anvil-production README for gtests-prod-2023-10-24-12-27-1 --- reports/anvil-production/README.md | 2 +- .../anvil-production/tool-tests/chunks.json | 10 +- .../gtests-prod-2023-10-24-12-27-1/chunk.json | 7 + .../gtests-prod-2023-10-24-12-27-1/chunk.txt | 15 + .../gtests-prod-2023-10-24-12-27-1/jobs.txt | 167 ++++ .../results.html | 291 +++++++ .../results.json | 1 + .../results.xunit | 820 ++++++++++++++++++ .../gtests-prod-2023-10-24-12-27-1/tools.yml | 92 ++ 9 files changed, 1399 insertions(+), 6 deletions(-) create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/chunk.json create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/chunk.txt create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/jobs.txt create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.html create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.json create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.xunit create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/tools.yml diff --git a/reports/anvil-production/README.md b/reports/anvil-production/README.md index e48d63ca4..50c97d411 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 Oct 23 00:43:46 2023Mon Oct 16 00:43:57 2023
1ToolsetMon Oct 23 12:45:56 2023Mon Oct 16 12:47:48 2023
2ToolsetTue Oct 24 00:43:01 2023Tue Oct 17 00:42:55 2023
3ToolsetTue Oct 17 12:46:22 2023Tue Oct 03 12:45:41 2023
4ToolsetWed Oct 18 00:42:46 2023Wed Oct 11 00:43:18 2023
5ToolsetWed Oct 18 12:46:09 2023Wed Oct 11 12:46:24 2023
6ToolsetThu Oct 19 00:43:39 2023Thu Oct 12 00:41:21 2023
7ToolsetThu Oct 19 12:46:05 2023Thu Oct 12 12:46:26 2023
8ToolsetFri Oct 20 00:42:08 2023Fri Oct 13 00:43:24 2023
9ToolsetFri Oct 20 12:44:37 2023Fri Oct 13 12:45:38 2023
10ToolsetSat Oct 21 00:41:52 2023Sat Oct 14 00:41:31 2023
11ToolsetSat Oct 21 12:43:13 2023Sat Oct 14 12:42:02 2023
12ToolsetSun Oct 22 00:45:03 2023Sun Oct 15 00:45:27 2023
13ToolsetSun Oct 22 12:42:28 2023Sun Oct 15 12:42:34 2023
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Oct 23 00:43:46 2023Mon Oct 16 00:43:57 2023
1ToolsetMon Oct 23 12:45:56 2023Mon Oct 16 12:47:48 2023
2ToolsetTue Oct 24 00:43:01 2023Tue Oct 17 00:42:55 2023
3ToolsetTue Oct 24 12:45:08 2023Tue Oct 17 12:46:22 2023
4ToolsetWed Oct 18 00:42:46 2023Wed Oct 11 00:43:18 2023
5ToolsetWed Oct 18 12:46:09 2023Wed Oct 11 12:46:24 2023
6ToolsetThu Oct 19 00:43:39 2023Thu Oct 12 00:41:21 2023
7ToolsetThu Oct 19 12:46:05 2023Thu Oct 12 12:46:26 2023
8ToolsetFri Oct 20 00:42:08 2023Fri Oct 13 00:43:24 2023
9ToolsetFri Oct 20 12:44:37 2023Fri Oct 13 12:45:38 2023
10ToolsetSat Oct 21 00:41:52 2023Sat Oct 14 00:41:31 2023
11ToolsetSat Oct 21 12:43:13 2023Sat Oct 14 12:42:02 2023
12ToolsetSun Oct 22 00:45:03 2023Sun Oct 15 00:45:27 2023
13ToolsetSun Oct 22 12:42:28 2023Sun Oct 15 12:42:34 2023
diff --git a/reports/anvil-production/tool-tests/chunks.json b/reports/anvil-production/tool-tests/chunks.json index eef858cb8..905f5dcbe 100644 --- a/reports/anvil-production/tool-tests/chunks.json +++ b/reports/anvil-production/tool-tests/chunks.json @@ -28,11 +28,11 @@ "date2": "Sun Oct 15 00:45:27 2023" }, "3": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-17-12-28-1/results.html", - "date1": "Tue Oct 17 12:46:22 2023", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-17-12-28-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-03-12-28-1/results.html", - "date2": "Tue Oct 03 12:45:41 2023" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.html", + "date1": "Tue Oct 24 12:45:08 2023", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-17-12-28-1/results.html", + "date2": "Tue Oct 17 12:46:22 2023" }, "1": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-23-12-28-1/results.html", diff --git a/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/chunk.json b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/chunk.json new file mode 100644 index 000000000..5f6bd8936 --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/chunk.json @@ -0,0 +1,7 @@ +{ + "3": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.html", + "date1": "Tue Oct 24 12:45:08 2023", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/chunk.txt b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/chunk.txt new file mode 100644 index 000000000..780536557 --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/chunk.txt @@ -0,0 +1,15 @@ +-t split_file_to_collection --tool-version 6cbe2f30c2d7 +-t reshape2_melt --tool-version 317ed0ee8bf2 +-t fasta_compute_length --tool-version 7d37cfda8e00 +-t bamtools --tool-version 4d343c1f606b +-t samtools_idxstats --tool-version 7a6034296ae9 +-t bcftools_gtcheck --tool-version 672b6c02fbc7 +-t bcftools_reheader --tool-version 9ef52d95114b +-t bcftools_plugin_tag2tag --tool-version bdfdf5f6e950 +-t vcfgenotypes --tool-version a60ae8af21a1 +-t flye --tool-version 3ee0ef312022 +-t poretools_tabular --tool-version 2cb2feb94f0e +-t deeptools_multi_bigwig_summary --tool-version 3c9f0c486cca +-t unicycler --tool-version 9e3e80cc4ad4 +-t ivar_removereads --tool-version ee2beb764a7b +-t hisat2 --tool-version 26371a1df031 diff --git a/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/jobs.txt b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/jobs.txt new file mode 100644 index 000000000..732cd5d82 --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/jobs.txt @@ -0,0 +1,167 @@ +a536e486e3bf0b12 ok 2023-10-24T15:26:07.773973 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a/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.html b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.html new file mode 100644 index 000000000..64a086fbd --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
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+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.json b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.json new file mode 100644 index 000000000..a6cb6d540 --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 68, "errors": 0, "failures": 1, "skips": 2}, "tests": [{"id": "bamtools/2.4.0.0-0", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.4.0.0", "test_index": 0, "time_seconds": 136.79665517807007, "inputs": {"input_bams": {"src": "hda", "id": "d41ea9bee51f4c04"}, "analysis_type|format_type|reference_source|ref_file": {"src": "hda", "id": "7b8190958cf7bdd8"}, "analysis_type|format_type|reference_source|reference_source_selector": "history", "analysis_type|format_type|mapqual": true, "analysis_type|format_type|format_type_selector": "pileup", "analysis_type|analysis_type_selector": "convert"}, "job": {"model_class": "Job", "id": "104bcefc6805908c", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:35:25.391532", "create_time": "2023-10-24T13:33:20.279586", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0", "history_id": "639c57257ba4f009", "external_id": "gxy-w7jk2", "command_line": "ln -s '/galaxy/server/database/objects/4/4/5/dataset_445d4352-9bbc-4683-b4d8-ade2748743d7.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/a/7/9/metadata_a79797db-bd6d-425b-b740-3bd21d87690f.dat' localbam.bam.bai && ln -s '/galaxy/server/database/objects/f/d/6/dataset_fd6aeb1b-ef96-4b47-ab4c-d836f12beeca.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo 'Error running samtools faidx for bamtools convert' >&2 && bamtools convert -format pileup -mapqual -fasta 'localref.fa' -out '/galaxy/server/database/objects/c/6/e/dataset_c6e1671d-4ee8-4649-9349-cc80fac8ae09.dat' -in localbam.bam", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"convert\", \"format_type\": {\"__current_case__\": 5, \"format_type_selector\": \"pileup\", \"mapqual\": \"true\", \"reference_source\": {\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 93, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}}}"}, "inputs": {"input_bams": {"id": "d41ea9bee51f4c04", "src": "hda", "uuid": "445d4352-9bbc-4683-b4d8-ade2748743d7"}, "analysis_type|format_type|ref_file": {"id": "7b8190958cf7bdd8", "src": "hda", "uuid": "fd6aeb1b-ef96-4b47-ab4c-d836f12beeca"}}, "outputs": {"out_file1": {"id": "9ff7ed69fb6e803a", "src": "hda", "uuid": "c6e1671d-4ee8-4649-9349-cc80fac8ae09"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "Pileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\n", "stderr": "\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\n", "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:35:15", "plugin": "core", "name": "start_epoch", "raw_value": "1698154515.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:35:15", "plugin": "core", "name": "end_epoch", "raw_value": "1698154515.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "bamtools/2.4.0.0-1", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.4.0.0", "test_index": 1, "time_seconds": 125.47643542289734, "inputs": {"input_bams": {"src": "hda", "id": "450365f003f18a7f"}, "analysis_type|analysis_type_selector": "count"}, "job": {"model_class": "Job", "id": "6a6303a31758e35c", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:37:31.017588", "create_time": "2023-10-24T13:35:35.807363", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0", "history_id": "639c57257ba4f009", "external_id": "gxy-q6s8h", "command_line": "ln -s '/galaxy/server/database/objects/5/4/8/dataset_5486c3e2-774d-4490-b476-334729cabde9.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/6/d/e/metadata_6de4256f-d032-4b46-9002-528335ff250d.dat' localbam.bam.bai && bamtools count > '/galaxy/server/database/objects/c/9/7/dataset_c972e2a7-4aff-4ce6-9732-110bd7dedb0a.dat' -in localbam.bam", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 1, \"analysis_type_selector\": \"count\"}"}, "inputs": {"input_bams": {"id": "450365f003f18a7f", "src": "hda", "uuid": "5486c3e2-774d-4490-b476-334729cabde9"}}, "outputs": {"out_file1": {"id": "e796f9d9ed4bde3f", "src": "hda", "uuid": "c972e2a7-4aff-4ce6-9732-110bd7dedb0a"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:37:21", "plugin": "core", "name": "start_epoch", "raw_value": "1698154641.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:37:21", "plugin": "core", "name": "end_epoch", "raw_value": "1698154641.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "bamtools/2.4.0.0-2", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.4.0.0", "test_index": 2, "time_seconds": 127.48451685905457, "inputs": {"input_bams": {"src": "hda", "id": "11b06594d0ddc5e4"}, "analysis_type|analysis_type_selector": "coverage"}, "job": {"model_class": "Job", "id": "b80f7e3aa89e8c14", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:39:38.397967", "create_time": "2023-10-24T13:37:42.044377", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0", "history_id": "639c57257ba4f009", "external_id": "gxy-ghj4c", "command_line": "ln -s '/galaxy/server/database/objects/6/9/b/dataset_69b91699-d44c-45eb-9798-f2e4c637a4e3.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/d/7/c/metadata_d7cc4b7a-2297-4186-b005-5c61898199f4.dat' localbam.bam.bai && bamtools coverage -out '/galaxy/server/database/objects/3/7/e/dataset_37e6e172-e9b5-4a88-9313-4c8e74b5edc2.dat' -in localbam.bam", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 2, \"analysis_type_selector\": \"coverage\"}"}, "inputs": {"input_bams": {"id": "11b06594d0ddc5e4", "src": "hda", "uuid": "69b91699-d44c-45eb-9798-f2e4c637a4e3"}}, "outputs": {"out_file1": {"id": "052debf6aa673a94", "src": "hda", "uuid": "37e6e172-e9b5-4a88-9313-4c8e74b5edc2"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "Pileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\n", "stderr": "\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\n", "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:39:29", "plugin": "core", "name": "start_epoch", "raw_value": "1698154769.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:39:29", "plugin": "core", "name": "end_epoch", "raw_value": "1698154769.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "bamtools/2.4.0.0-3", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.4.0.0", "test_index": 3, "time_seconds": 131.1454930305481, "inputs": {"input_bams": {"src": "hda", "id": "1b0464b6e7d4db86"}, "analysis_type|analysis_type_selector": "header"}, "job": {"model_class": "Job", "id": "3d9b326f0a2de686", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:41:49.466882", "create_time": "2023-10-24T13:39:49.260610", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0", "history_id": "639c57257ba4f009", "external_id": "gxy-285ds", "command_line": "ln -s '/galaxy/server/database/objects/4/7/0/dataset_470af2ed-f8f2-48da-89a1-b0840a4a7de9.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/e/e/c/metadata_eec4a93e-9f81-49cd-b958-027288e563f1.dat' localbam.bam.bai && bamtools header > '/galaxy/server/database/objects/b/d/1/dataset_bd1c60bd-9167-46eb-9ae9-4effe770493b.dat' -in localbam.bam", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 3, \"analysis_type_selector\": \"header\"}"}, "inputs": {"input_bams": {"id": "1b0464b6e7d4db86", "src": "hda", "uuid": "470af2ed-f8f2-48da-89a1-b0840a4a7de9"}}, "outputs": {"out_file1": {"id": "078eacbf24b1c667", "src": "hda", "uuid": "bd1c60bd-9167-46eb-9ae9-4effe770493b"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:41:40", "plugin": "core", "name": "start_epoch", "raw_value": "1698154900.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:41:40", "plugin": "core", "name": "end_epoch", "raw_value": "1698154900.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "bcftools_gtcheck/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_gtcheck", "tool_version": "1.10", "test_index": 0, "time_seconds": 134.82347512245178, "inputs": {"input_file": {"src": "hda", "id": "66cff3a3ab4618bf"}, "sec_default|GTs_only": "99"}, "job": {"model_class": "Job", "id": "4f22e28d648b2f46", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:48:37.049689", "create_time": "2023-10-24T13:46:33.047129", "galaxy_version": "21.09", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10", "history_id": "639c57257ba4f009", "external_id": "gxy-flfnp", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/1/f/dataset_51fe78ca-9a8a-4bea-8613-357f1239dddc.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools gtcheck --GTs-only '99' input.vcf.gz > '/galaxy/server/database/objects/0/1/c/dataset_01ce83ba-481f-472c-bf27-fd7e01bd0bd5.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_default": "{\"GTs_only\": \"99\", \"all_sites\": \"false\", \"genotypes\": null, \"homs_only\": \"false\", \"plot\": \"\", \"query_sample\": null, \"target_sample\": null}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_file": {"id": "66cff3a3ab4618bf", "src": "hda", "uuid": "51fe78ca-9a8a-4bea-8613-357f1239dddc"}}, "outputs": {"output_file": {"id": "95f8d70911d46dda", "src": "hda", "uuid": "01ce83ba-481f-472c-bf27-fd7e01bd0bd5"}}, "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": "2023-10-24 13:48:26", "plugin": "core", "name": "end_epoch", "raw_value": "1698155306.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:48:25", "plugin": "core", "name": "start_epoch", "raw_value": "1698155305.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_plugin_tag2tag/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_tag2tag", "tool_version": "1.10", "test_index": 0, "time_seconds": 130.52589082717896, "inputs": {"input_file": {"src": "hda", "id": "58a6cf93e1167086"}, "sec_plugin|conversion": "--gl-to-pl", "sec_plugin|replace": true, "output_type": "v"}, "job": {"model_class": "Job", "id": "72e076ef074a47a3", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:57:34.594308", "create_time": "2023-10-24T13:55:34.627493", "galaxy_version": "21.09", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10", "history_id": "639c57257ba4f009", "external_id": "gxy-8t2d4", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/9/1/0/dataset_91095c75-32a2-4658-b01e-8b2b3dd317b7.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin tag2tag --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz -- --gl-to-pl --replace > '/galaxy/server/database/objects/f/4/6/dataset_f4624053-5ee2-4105-95ef-49057b0628ff.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"\": \"0.1\", \"conversion\": \"--gl-to-pl\", \"replace\": \"true\"}", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_file": {"id": "58a6cf93e1167086", "src": "hda", "uuid": "91095c75-32a2-4658-b01e-8b2b3dd317b7"}}, "outputs": {"output_file": {"id": "128787d8e2cf1a32", "src": "hda", "uuid": "f4624053-5ee2-4105-95ef-49057b0628ff"}}, "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": "2023-10-24 13:57:25", "plugin": "core", "name": "end_epoch", "raw_value": "1698155845.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:57:25", "plugin": "core", "name": "start_epoch", "raw_value": "1698155845.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_reheader/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_reheader", "tool_version": "1.10", "test_index": 0, "time_seconds": 141.21354627609253, "inputs": {"input_file": {"src": "hda", "id": "9ff33426c808d49c"}, "sec_default|header": {"src": "hda", "id": "fc056071e41fde5e"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "6bd4eb180716bded", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:50:59.380548", "create_time": "2023-10-24T13:48:51.024218", "galaxy_version": "21.09", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10", "history_id": "639c57257ba4f009", "external_id": "gxy-zwm5d", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/e/8/4/dataset_e84311e4-46bd-46ea-a7f7-193514b41f7b.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools reheader --header \"/galaxy/server/database/objects/7/6/5/dataset_765a0526-81ec-415c-82f9-4eb31aeb3f14.dat\" input.vcf.gz | bcftools view --output-type 'v' > '/galaxy/server/database/objects/5/7/f/dataset_57f486d1-4039-4e22-8a4a-21bebdeba4d9.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"header\": {\"values\": [{\"id\": 108, \"src\": \"hda\"}]}, \"rename_samples\": {\"__current_case__\": 0, \"samples_src\": \"none\"}}"}, "inputs": {"input_file": {"id": "9ff33426c808d49c", "src": "hda", "uuid": "e84311e4-46bd-46ea-a7f7-193514b41f7b"}, "header": {"id": "fc056071e41fde5e", "src": "hda", "uuid": "765a0526-81ec-415c-82f9-4eb31aeb3f14"}}, "outputs": {"output_file": {"id": "ecd3a10224753a8c", "src": "hda", "uuid": "57f486d1-4039-4e22-8a4a-21bebdeba4d9"}}, "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": "2023-10-24 13:50:49", "plugin": "core", "name": "end_epoch", "raw_value": "1698155449.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:50:49", "plugin": "core", "name": "start_epoch", "raw_value": "1698155449.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_reheader/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_reheader", "tool_version": "1.10", "test_index": 1, "time_seconds": 129.31236052513123, "inputs": {"input_file": {"src": "hda", "id": "9a638de4d9065033"}, "sec_default|rename_samples|sample_file": {"src": "hda", "id": "6ddd94d8ad84c427"}, "sec_default|rename_samples|samples_src": "history", "output_type": "v"}, "job": {"model_class": "Job", "id": "d18b1d153041ab26", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:53:08.821044", "create_time": "2023-10-24T13:51:10.416817", "galaxy_version": "21.09", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10", "history_id": "639c57257ba4f009", "external_id": "gxy-v44gv", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/b/b/3/dataset_bb3f46d9-21f9-44dd-99cf-c15ef9b01e0d.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools reheader --samples \"/galaxy/server/database/objects/c/a/0/dataset_ca0980e7-4753-4216-87b2-1c1d9fb90ec7.dat\" input.vcf.gz | bcftools view --output-type 'v' > '/galaxy/server/database/objects/8/2/c/dataset_82c3cb4d-38e9-47db-b4d0-717a69301046.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"header\": null, \"rename_samples\": {\"__current_case__\": 1, \"sample_file\": {\"values\": [{\"id\": 111, \"src\": \"hda\"}]}, \"samples_src\": \"history\"}}"}, "inputs": {"input_file": {"id": "9a638de4d9065033", "src": "hda", "uuid": "bb3f46d9-21f9-44dd-99cf-c15ef9b01e0d"}, "sec_default|sample_file": {"id": "6ddd94d8ad84c427", "src": "hda", "uuid": "ca0980e7-4753-4216-87b2-1c1d9fb90ec7"}}, "outputs": {"output_file": {"id": "59a25c08373d0c2f", "src": "hda", "uuid": "82c3cb4d-38e9-47db-b4d0-717a69301046"}}, "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": "2023-10-24 13:52:59", "plugin": "core", "name": "end_epoch", "raw_value": "1698155579.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:52:59", "plugin": "core", "name": "start_epoch", "raw_value": "1698155579.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_reheader/1.10-2", "has_data": true, "data": {"tool_id": "bcftools_reheader", "tool_version": "1.10", "test_index": 2, "time_seconds": 133.47032761573792, "inputs": {"input_file": {"src": "hda", "id": "51c25f1caa684f9b"}, "sec_default|rename_samples|sample_file": {"src": "hda", "id": "60cebd90c87fbbaf"}, "sec_default|rename_samples|samples_src": "history", "output_type": "v"}, "job": {"model_class": "Job", "id": "5ae9b4b1aa3dde57", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:55:22.454808", "create_time": "2023-10-24T13:53:20.225537", "galaxy_version": "21.09", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10", "history_id": "639c57257ba4f009", "external_id": "gxy-k59k9", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/3/d/dataset_83d92fd8-1e01-44e3-8cb8-ff6a3ae1d0d0.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools reheader --samples \"/galaxy/server/database/objects/8/2/0/dataset_82056f68-6dc4-4b56-88fa-16fd522a2adb.dat\" input.vcf.gz | bcftools view --output-type 'v' > '/galaxy/server/database/objects/6/6/7/dataset_667227e2-03e8-4e45-9ecd-b281aab597ca.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"header\": null, \"rename_samples\": {\"__current_case__\": 1, \"sample_file\": {\"values\": [{\"id\": 114, \"src\": \"hda\"}]}, \"samples_src\": \"history\"}}"}, "inputs": {"input_file": {"id": "51c25f1caa684f9b", "src": "hda", "uuid": "83d92fd8-1e01-44e3-8cb8-ff6a3ae1d0d0"}, "sec_default|sample_file": {"id": "60cebd90c87fbbaf", "src": "hda", "uuid": "82056f68-6dc4-4b56-88fa-16fd522a2adb"}}, "outputs": {"output_file": {"id": "08e3c1ab61966b84", "src": "hda", "uuid": "667227e2-03e8-4e45-9ecd-b281aab597ca"}}, "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": "2023-10-24 13:55:12", "plugin": "core", "name": "end_epoch", "raw_value": "1698155712.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:55:12", "plugin": "core", "name": "start_epoch", "raw_value": "1698155712.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_multi_bigwig_summary/3.3.2.0.0-0", "has_data": true, "data": {"tool_id": "deeptools_multi_bigwig_summary", "tool_version": "3.3.2.0.0", "test_index": 0, "time_seconds": 158.57856154441833, "inputs": {"multibigwig_conditional|bigwigfiles": [{"src": "hda", "id": "fdde2a11ed14d114"}, {"src": "hda", "id": "fdde2a11ed14d114"}], "mode|binSize": "10", "mode|modeOpt": "bins"}, "job": {"model_class": "Job", "id": "d41ea9bee51f4c04", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:30:22.108021", "create_time": "2023-10-24T14:27:53.845231", "galaxy_version": "21.09", "command_version": "multiBigwigSummary 3.3.2", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.3.2.0.0", "history_id": "639c57257ba4f009", "external_id": "gxy-2vfnz", "command_line": "ln -f -s '/galaxy/server/database/objects/e/0/e/dataset_e0e4e06d-7c3c-40ac-9c80-3d24b7f4444e.dat' 'test.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/e/0/e/dataset_e0e4e06d-7c3c-40ac-9c80-3d24b7f4444e.dat' 'test.bw_1.bw' && multiBigwigSummary bins --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --outFileName /galaxy/server/database/objects/4/2/e/dataset_42e7afa5-d4bf-4b61-b10d-b62986bd6330.dat --bwfiles 'test.bw_0.bw' 'test.bw_1.bw' --labels 'test.bw' 'test.bw' --binSize '10' --distanceBetweenBins '0'", "traceback": null, "params": {"__input_ext": "\"bigwig\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "outRawCounts": "\"false\"", "region": "\"\"", "mode": "{\"__current_case__\": 0, \"binSize\": \"10\", \"distanceBetweenBins\": \"0\", \"modeOpt\": \"bins\"}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibigwig_conditional": "{\"__current_case__\": 0, \"bigwigfiles\": {\"values\": [{\"id\": 154, \"src\": \"hda\"}, {\"id\": 154, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"bigwigfiles": {"id": "fdde2a11ed14d114", "src": "hda", "uuid": "e0e4e06d-7c3c-40ac-9c80-3d24b7f4444e"}, "bigwigfiles1": {"id": "fdde2a11ed14d114", "src": "hda", "uuid": "e0e4e06d-7c3c-40ac-9c80-3d24b7f4444e"}, "bigwigfiles2": {"id": "fdde2a11ed14d114", "src": "hda", "uuid": "e0e4e06d-7c3c-40ac-9c80-3d24b7f4444e"}}, "outputs": {"outFile": {"id": "ab80dd031322ef0b", "src": "hda", "uuid": "42e7afa5-d4bf-4b61-b10d-b62986bd6330"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "Number of bins found: 120\n", "stderr": "\nNumber of bins found: 120\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": "2023-10-24 14:30:05", "plugin": "core", "name": "end_epoch", "raw_value": "1698157805.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:30:05", "plugin": "core", "name": "start_epoch", "raw_value": "1698157805.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "fasta_compute_length/1.0.3-0", "has_data": true, "data": {"tool_id": "fasta_compute_length", "tool_version": "1.0.3", "test_index": 0, "time_seconds": 140.9165234565735, "inputs": {"ref|input": {"src": "hda", "id": "67b028c597d773cb"}, "ref|keep_first": "0", "ref|keep_first_word": false}, "job": {"model_class": "Job", "id": "a8f83ae8df4c8e27", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:28:39.306032", "create_time": "2023-10-24T13:26:29.399050", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3", "history_id": "639c57257ba4f009", "external_id": "gxy-x54hp", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/fasta_compute_length/fasta_compute_length.py' '/galaxy/server/database/objects/4/5/e/dataset_45e93c90-041b-43ee-bb5d-48e3a163ce36.dat' '/galaxy/server/database/objects/b/9/0/dataset_b90e25e7-8d1e-45c3-b52d-b7131ab17b15.dat' 0 id_and_desc", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ref": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 86, \"src\": \"hda\"}]}, \"keep_first\": \"0\", \"keep_first_word\": \"false\", \"ref_source\": \"history\"}"}, "inputs": {"input": {"id": "67b028c597d773cb", "src": "hda", "uuid": "45e93c90-041b-43ee-bb5d-48e3a163ce36"}}, "outputs": {"output": {"id": "56f2bcdddf4392f6", "src": "hda", "uuid": "b90e25e7-8d1e-45c3-b52d-b7131ab17b15"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:28:28", "plugin": "core", "name": "start_epoch", "raw_value": "1698154108.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:28:28", "plugin": "core", "name": "end_epoch", "raw_value": "1698154108.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fasta_compute_length/1.0.3-1", "has_data": true, "data": {"tool_id": "fasta_compute_length", "tool_version": "1.0.3", "test_index": 1, "time_seconds": 135.50512862205505, "inputs": {"ref|input": {"src": "hda", "id": "325936b148b10c36"}, "ref|keep_first": "0", "ref|keep_first_word": false}, "job": {"model_class": "Job", "id": "6fd968aa0d679677", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:30:54.858996", "create_time": "2023-10-24T13:28:50.674927", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3", "history_id": "639c57257ba4f009", "external_id": "gxy-nnf2h", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/fasta_compute_length/fasta_compute_length.py' '/galaxy/server/database/objects/8/6/5/dataset_865fb0f1-fda5-4eba-8aa6-ead43c1e25c8.dat' '/galaxy/server/database/objects/9/2/6/dataset_926d665f-7b3b-42a6-b1fc-f2883b4b4c6d.dat' 0 id_and_desc", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ref": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 88, \"src\": \"hda\"}]}, \"keep_first\": \"0\", \"keep_first_word\": \"false\", \"ref_source\": \"history\"}"}, "inputs": {"input": {"id": "325936b148b10c36", "src": "hda", "uuid": "865fb0f1-fda5-4eba-8aa6-ead43c1e25c8"}}, "outputs": {"output": {"id": "5cdae4e952cf3fee", "src": "hda", "uuid": "926d665f-7b3b-42a6-b1fc-f2883b4b4c6d"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:30:44", "plugin": "core", "name": "start_epoch", "raw_value": "1698154244.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:30:44", "plugin": "core", "name": "end_epoch", "raw_value": "1698154244.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fasta_compute_length/1.0.3-2", "has_data": true, "data": {"tool_id": "fasta_compute_length", "tool_version": "1.0.3", "test_index": 2, "time_seconds": 131.93199563026428, "inputs": {"ref|input": {"src": "hda", "id": "51a7318c135d87ee"}, "ref|keep_first": "14", "ref|keep_first_word": false}, "job": {"model_class": "Job", "id": "bbbb1b84556c6414", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:33:07.059493", "create_time": "2023-10-24T13:31:06.670477", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3", "history_id": "639c57257ba4f009", "external_id": "gxy-qsgmp", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/fasta_compute_length/fasta_compute_length.py' '/galaxy/server/database/objects/7/c/3/dataset_7c32f7f8-5cfb-4328-a0b4-3b909713e148.dat' '/galaxy/server/database/objects/5/4/1/dataset_5418bf29-8e7d-495c-b9bb-b8cd44006ff9.dat' 14 id_and_desc", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ref": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 90, \"src\": \"hda\"}]}, \"keep_first\": \"14\", \"keep_first_word\": \"false\", \"ref_source\": \"history\"}"}, "inputs": {"input": {"id": "51a7318c135d87ee", "src": "hda", "uuid": "7c32f7f8-5cfb-4328-a0b4-3b909713e148"}}, "outputs": {"output": {"id": "48967b3c65d8aba5", "src": "hda", "uuid": "5418bf29-8e7d-495c-b9bb-b8cd44006ff9"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:32:57", "plugin": "core", "name": "start_epoch", "raw_value": "1698154377.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:32:57", "plugin": "core", "name": "end_epoch", "raw_value": "1698154377.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fasta_compute_length/1.0.3-3", "has_data": true, "data": {"tool_id": "fasta_compute_length", "tool_version": "1.0.3", "test_index": 3, "status": "skip"}}, {"id": "fasta_compute_length/1.0.3-4", "has_data": true, "data": {"tool_id": "fasta_compute_length", "tool_version": "1.0.3", "test_index": 4, "status": "skip"}}, {"id": "flye/2.6-0", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.6", "test_index": 0, "time_seconds": 248.26837849617004, "inputs": {"inputs": {"src": "hda", "id": "739cf057da645fe3"}, "mode": "--pacbio-raw", "g": "10000"}, "job": {"model_class": "Job", "id": "fb065f9e39b7e79b", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:04:02.100815", "create_time": "2023-10-24T14:00:08.306540", "galaxy_version": "21.09", "command_version": "2.6-release", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6", "history_id": "639c57257ba4f009", "external_id": "gxy-9w2c4", "command_line": "ln -s '/galaxy/server/database/objects/b/8/4/dataset_b8498808-4f4b-449c-bb38-5af104dbd737.dat' ./input_0.fasta && flye --pacbio-raw ./input_0.fasta -o out_dir -g '10000' -t ${GALAXY_SLOTS:-4} -i 1 2>&1", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "no_trestle": "\"false\"", "meta": "\"false\"", "plasmids": "\"false\"", "asm": "\"\"", "m": "\"\"", "i": "\"1\"", "g": "\"10000\"", "mode": "\"--pacbio-raw\""}, "inputs": {"inputs": {"id": "739cf057da645fe3", "src": "hda", "uuid": "b8498808-4f4b-449c-bb38-5af104dbd737"}}, "outputs": {"consensus": {"id": "c8b80a7cdbdbfc9c", "src": "hda", "uuid": "5b742703-b868-423e-a179-88620b0bca9f"}, "assembly_graph": {"id": "94d7311e00b41c34", "src": "hda", "uuid": "32e2c67d-6c74-4096-a1e3-3b37495cb6d6"}, "assembly_gfa": {"id": "d8e41928ae2102ed", "src": "hda", "uuid": "aed9b329-51d8-47be-ba37-d59d56a0893d"}, "assembly_info": {"id": "ad40023effa91a45", "src": "hda", "uuid": "1fd23ec7-b3a7-4b3c-9213-863de308b9e3"}, "flye_log": {"id": "1fb4ef9e770e1a6d", "src": "hda", "uuid": "c4460bbb-c757-46c8-85eb-caec6f1036b0"}}, "output_collections": {}, "tool_stdout": "[2023-10-24 14:02:08] INFO: Starting Flye 2.6-release\n[2023-10-24 14:02:08] INFO: >>>STAGE: configure\n[2023-10-24 14:02:08] INFO: Configuring run\n[2023-10-24 14:02:08] INFO: Total read length: 1466260\n[2023-10-24 14:02:08] INFO: Input genome size: 10000\n[2023-10-24 14:02:08] INFO: Estimated coverage: 146\n[2023-10-24 14:02:08] INFO: Reads N50/N90: 9054 / 4697\n[2023-10-24 14:02:08] INFO: Minimum overlap set to 5000\n[2023-10-24 14:02:08] INFO: Selected k-mer size: 15\n[2023-10-24 14:02:08] INFO: >>>STAGE: assembly\n[2023-10-24 14:02:08] INFO: Assembling disjointigs\n[2023-10-24 14:02:08] INFO: Reading sequences\n[2023-10-24 14:02:08] INFO: Generating solid k-mer index\n[2023-10-24 14:02:30] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:02:30] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:02:30] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:02:55] INFO: Extending reads\n[2023-10-24 14:02:58] INFO: Overlap-based coverage: 25\n[2023-10-24 14:02:58] INFO: Median overlap divergence: 0.169224\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:02:59] INFO: Assembled 1 disjointigs\n[2023-10-24 14:02:59] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2023-10-24 14:03:00] INFO: >>>STAGE: consensus\n[2023-10-24 14:03:00] INFO: Running Minimap2\n[2023-10-24 14:03:01] INFO: Computing consensus\n[2023-10-24 14:03:02] INFO: Alignment error rate: 0.156879\n[2023-10-24 14:03:02] INFO: >>>STAGE: repeat\n[2023-10-24 14:03:02] INFO: Building and resolving repeat graph\n[2023-10-24 14:03:02] INFO: Reading sequences\n[2023-10-24 14:03:02] INFO: Building repeat graph\n50% 100% \n[2023-10-24 14:03:24] INFO: Median overlap divergence: 0\n[2023-10-24 14:03:24] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:03:47] INFO: Aligned read sequence: 1184744 / 1313105 (0.902246)\n[2023-10-24 14:03:47] INFO: Median overlap divergence: 0.0616647\n[2023-10-24 14:03:47] INFO: Mean edge coverage: 29\n[2023-10-24 14:03:47] INFO: Resolving repeats\n[2023-10-24 14:03:47] INFO: >>>STAGE: trestle\n[2023-10-24 14:03:47] INFO: Simple unbridged repeats: 0\n[2023-10-24 14:03:47] INFO: Resolved: 0\n[2023-10-24 14:03:47] INFO: >>>STAGE: contigger\n[2023-10-24 14:03:47] INFO: Generating contigs\n[2023-10-24 14:03:47] INFO: Reading sequences\n[2023-10-24 14:03:47] INFO: Generated 1 contigs\n[2023-10-24 14:03:47] INFO: Added 0 scaffold connections\n[2023-10-24 14:03:47] INFO: >>>STAGE: polishing\n[2023-10-24 14:03:47] INFO: Polishing genome (1/1)\n[2023-10-24 14:03:47] INFO: Running minimap2\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a453730000004c'\n[2023-10-24 14:03:48] INFO: Separating alignment into bubbles\n[2023-10-24 14:03:49] INFO: Alignment error rate: 0.104507\n[2023-10-24 14:03:49] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a4538a0000004d'\n[2023-10-24 14:03:52] INFO: >>>STAGE: finalize\n[2023-10-24 14:03:53] INFO: Assembly statistics:\n\n\tTotal length:\t39944\n\tFragments:\t1\n\tFragments N50:\t39944\n\tLargest frg:\t39944\n\tScaffolds:\t0\n\tMean coverage:\t27\n\n[2023-10-24 14:03:53] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/74/working/out_dir/assembly.fasta\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "[2023-10-24 14:02:08] INFO: Starting Flye 2.6-release\n[2023-10-24 14:02:08] INFO: >>>STAGE: configure\n[2023-10-24 14:02:08] INFO: Configuring run\n[2023-10-24 14:02:08] INFO: Total read length: 1466260\n[2023-10-24 14:02:08] INFO: Input genome size: 10000\n[2023-10-24 14:02:08] INFO: Estimated coverage: 146\n[2023-10-24 14:02:08] INFO: Reads N50/N90: 9054 / 4697\n[2023-10-24 14:02:08] INFO: Minimum overlap set to 5000\n[2023-10-24 14:02:08] INFO: Selected k-mer size: 15\n[2023-10-24 14:02:08] INFO: >>>STAGE: assembly\n[2023-10-24 14:02:08] INFO: Assembling disjointigs\n[2023-10-24 14:02:08] INFO: Reading sequences\n[2023-10-24 14:02:08] INFO: Generating solid k-mer index\n[2023-10-24 14:02:30] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:02:30] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:02:30] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:02:55] INFO: Extending reads\n[2023-10-24 14:02:58] INFO: Overlap-based coverage: 25\n[2023-10-24 14:02:58] INFO: Median overlap divergence: 0.169224\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:02:59] INFO: Assembled 1 disjointigs\n[2023-10-24 14:02:59] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2023-10-24 14:03:00] INFO: >>>STAGE: consensus\n[2023-10-24 14:03:00] INFO: Running Minimap2\n[2023-10-24 14:03:01] INFO: Computing consensus\n[2023-10-24 14:03:02] INFO: Alignment error rate: 0.156879\n[2023-10-24 14:03:02] INFO: >>>STAGE: repeat\n[2023-10-24 14:03:02] INFO: Building and resolving repeat graph\n[2023-10-24 14:03:02] INFO: Reading sequences\n[2023-10-24 14:03:02] INFO: Building repeat graph\n50% 100% \n[2023-10-24 14:03:24] INFO: Median overlap divergence: 0\n[2023-10-24 14:03:24] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:03:47] INFO: Aligned read sequence: 1184744 / 1313105 (0.902246)\n[2023-10-24 14:03:47] INFO: Median overlap divergence: 0.0616647\n[2023-10-24 14:03:47] INFO: Mean edge coverage: 29\n[2023-10-24 14:03:47] INFO: Resolving repeats\n[2023-10-24 14:03:47] INFO: >>>STAGE: trestle\n[2023-10-24 14:03:47] INFO: Simple unbridged repeats: 0\n[2023-10-24 14:03:47] INFO: Resolved: 0\n[2023-10-24 14:03:47] INFO: >>>STAGE: contigger\n[2023-10-24 14:03:47] INFO: Generating contigs\n[2023-10-24 14:03:47] INFO: Reading sequences\n[2023-10-24 14:03:47] INFO: Generated 1 contigs\n[2023-10-24 14:03:47] INFO: Added 0 scaffold connections\n[2023-10-24 14:03:47] INFO: >>>STAGE: polishing\n[2023-10-24 14:03:47] INFO: Polishing genome (1/1)\n[2023-10-24 14:03:47] INFO: Running minimap2\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a453730000004c'\n[2023-10-24 14:03:48] INFO: Separating alignment into bubbles\n[2023-10-24 14:03:49] INFO: Alignment error rate: 0.104507\n[2023-10-24 14:03:49] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a4538a0000004d'\n[2023-10-24 14:03:52] INFO: >>>STAGE: finalize\n[2023-10-24 14:03:53] INFO: Assembly statistics:\n\n\tTotal length:\t39944\n\tFragments:\t1\n\tFragments N50:\t39944\n\tLargest frg:\t39944\n\tScaffolds:\t0\n\tMean coverage:\t27\n\n[2023-10-24 14:03:53] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/74/working/out_dir/assembly.fasta\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "105.0000000"}, {"title": "Job End Time", "value": "2023-10-24 14:03:53", "plugin": "core", "name": "end_epoch", "raw_value": "1698156233.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:02:08", "plugin": "core", "name": "start_epoch", "raw_value": "1698156128.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "flye/2.6-1", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.6", "test_index": 1, "time_seconds": 238.4338767528534, "inputs": {"inputs": {"src": "hda", "id": "24fe3ed1e1efd09f"}, "mode": "--nano-raw", "g": "10000"}, "job": {"model_class": "Job", "id": "b4cb4228a1d2062b", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:08:00.562150", "create_time": "2023-10-24T14:04:15.051228", "galaxy_version": "21.09", "command_version": "2.6-release", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6", "history_id": "639c57257ba4f009", "external_id": "gxy-dqln4", "command_line": "ln -s '/galaxy/server/database/objects/8/9/d/dataset_89d26c0e-6dcc-4ccd-ab6b-a17dd8091f2c.dat' ./input_0.fasta && flye --nano-raw ./input_0.fasta -o out_dir -g '10000' -t ${GALAXY_SLOTS:-4} -i 1 2>&1", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "no_trestle": "\"false\"", "meta": "\"false\"", "plasmids": "\"false\"", "asm": "\"\"", "m": "\"\"", "i": "\"1\"", "g": "\"10000\"", "mode": "\"--nano-raw\""}, "inputs": {"inputs": {"id": "24fe3ed1e1efd09f", "src": "hda", "uuid": "89d26c0e-6dcc-4ccd-ab6b-a17dd8091f2c"}}, "outputs": {"consensus": {"id": "ee9ce26a63ca5c9f", "src": "hda", "uuid": "1a90af71-96ff-4bf0-a19b-5b903bde946e"}, "assembly_graph": {"id": "644661f6f911b6a8", "src": "hda", "uuid": "4ab899ec-32c0-4483-8251-dbed1d912767"}, "assembly_gfa": {"id": "94a1c0e7f09c2663", "src": "hda", "uuid": "5044eea6-d8b9-472a-8882-2838618f7721"}, "assembly_info": {"id": "408488441c69a820", "src": "hda", "uuid": "6650ec64-79dc-469f-a11d-a6200a320d7d"}, "flye_log": {"id": "ae1b404e546d0479", "src": "hda", "uuid": "a54ced40-db6d-410a-9f80-1209b39b23d2"}}, "output_collections": {}, "tool_stdout": "[2023-10-24 14:06:07] INFO: Starting Flye 2.6-release\n[2023-10-24 14:06:07] INFO: >>>STAGE: configure\n[2023-10-24 14:06:07] INFO: Configuring run\n[2023-10-24 14:06:07] INFO: Total read length: 1466260\n[2023-10-24 14:06:07] INFO: Input genome size: 10000\n[2023-10-24 14:06:07] INFO: Estimated coverage: 146\n[2023-10-24 14:06:07] INFO: Reads N50/N90: 9054 / 4697\n[2023-10-24 14:06:07] INFO: Minimum overlap set to 5000\n[2023-10-24 14:06:07] INFO: Selected k-mer size: 15\n[2023-10-24 14:06:07] INFO: >>>STAGE: assembly\n[2023-10-24 14:06:07] INFO: Assembling disjointigs\n[2023-10-24 14:06:07] INFO: Reading sequences\n[2023-10-24 14:06:07] INFO: Generating solid k-mer index\n[2023-10-24 14:06:29] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:06:29] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:06:30] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:06:54] INFO: Extending reads\n[2023-10-24 14:06:58] INFO: Overlap-based coverage: 25\n[2023-10-24 14:06:58] INFO: Median overlap divergence: 0.169224\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:06:58] INFO: Assembled 1 disjointigs\n[2023-10-24 14:06:58] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2023-10-24 14:07:00] INFO: >>>STAGE: consensus\n[2023-10-24 14:07:00] INFO: Running Minimap2\n[2023-10-24 14:07:00] INFO: Computing consensus\n[2023-10-24 14:07:01] INFO: Alignment error rate: 0.157030\n[2023-10-24 14:07:01] INFO: >>>STAGE: repeat\n[2023-10-24 14:07:01] INFO: Building and resolving repeat graph\n[2023-10-24 14:07:01] INFO: Reading sequences\n[2023-10-24 14:07:01] INFO: Building repeat graph\n50% 100% \n[2023-10-24 14:07:23] INFO: Median overlap divergence: 0\n[2023-10-24 14:07:23] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:07:46] INFO: Aligned read sequence: 1184737 / 1313105 (0.902241)\n[2023-10-24 14:07:46] INFO: Median overlap divergence: 0.0613459\n[2023-10-24 14:07:46] INFO: Mean edge coverage: 29\n[2023-10-24 14:07:46] INFO: Resolving repeats\n[2023-10-24 14:07:46] INFO: >>>STAGE: trestle\n[2023-10-24 14:07:46] INFO: Simple unbridged repeats: 0\n[2023-10-24 14:07:46] INFO: Resolved: 0\n[2023-10-24 14:07:46] INFO: >>>STAGE: contigger\n[2023-10-24 14:07:46] INFO: Generating contigs\n[2023-10-24 14:07:46] INFO: Reading sequences\n[2023-10-24 14:07:46] INFO: Generated 1 contigs\n[2023-10-24 14:07:46] INFO: Added 0 scaffold connections\n[2023-10-24 14:07:46] INFO: >>>STAGE: polishing\n[2023-10-24 14:07:46] INFO: Polishing genome (1/1)\n[2023-10-24 14:07:46] INFO: Running minimap2\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a453b500000051'\n[2023-10-24 14:07:47] INFO: Separating alignment into bubbles\n[2023-10-24 14:07:48] INFO: Alignment error rate: 0.104939\n[2023-10-24 14:07:48] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a453cc00000052'\n[2023-10-24 14:07:51] INFO: >>>STAGE: finalize\n[2023-10-24 14:07:51] INFO: Assembly statistics:\n\n\tTotal length:\t40419\n\tFragments:\t1\n\tFragments N50:\t40419\n\tLargest frg:\t40419\n\tScaffolds:\t0\n\tMean coverage:\t26\n\n[2023-10-24 14:07:51] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/76/working/out_dir/assembly.fasta\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "[2023-10-24 14:06:07] INFO: Starting Flye 2.6-release\n[2023-10-24 14:06:07] INFO: >>>STAGE: configure\n[2023-10-24 14:06:07] INFO: Configuring run\n[2023-10-24 14:06:07] INFO: Total read length: 1466260\n[2023-10-24 14:06:07] INFO: Input genome size: 10000\n[2023-10-24 14:06:07] INFO: Estimated coverage: 146\n[2023-10-24 14:06:07] INFO: Reads N50/N90: 9054 / 4697\n[2023-10-24 14:06:07] INFO: Minimum overlap set to 5000\n[2023-10-24 14:06:07] INFO: Selected k-mer size: 15\n[2023-10-24 14:06:07] INFO: >>>STAGE: assembly\n[2023-10-24 14:06:07] INFO: Assembling disjointigs\n[2023-10-24 14:06:07] INFO: Reading sequences\n[2023-10-24 14:06:07] INFO: Generating solid k-mer index\n[2023-10-24 14:06:29] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:06:29] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:06:30] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:06:54] INFO: Extending reads\n[2023-10-24 14:06:58] INFO: Overlap-based coverage: 25\n[2023-10-24 14:06:58] INFO: Median overlap divergence: 0.169224\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:06:58] INFO: Assembled 1 disjointigs\n[2023-10-24 14:06:58] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2023-10-24 14:07:00] INFO: >>>STAGE: consensus\n[2023-10-24 14:07:00] INFO: Running Minimap2\n[2023-10-24 14:07:00] INFO: Computing consensus\n[2023-10-24 14:07:01] INFO: Alignment error rate: 0.157030\n[2023-10-24 14:07:01] INFO: >>>STAGE: repeat\n[2023-10-24 14:07:01] INFO: Building and resolving repeat graph\n[2023-10-24 14:07:01] INFO: Reading sequences\n[2023-10-24 14:07:01] INFO: Building repeat graph\n50% 100% \n[2023-10-24 14:07:23] INFO: Median overlap divergence: 0\n[2023-10-24 14:07:23] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:07:46] INFO: Aligned read sequence: 1184737 / 1313105 (0.902241)\n[2023-10-24 14:07:46] INFO: Median overlap divergence: 0.0613459\n[2023-10-24 14:07:46] INFO: Mean edge coverage: 29\n[2023-10-24 14:07:46] INFO: Resolving repeats\n[2023-10-24 14:07:46] INFO: >>>STAGE: trestle\n[2023-10-24 14:07:46] INFO: Simple unbridged repeats: 0\n[2023-10-24 14:07:46] INFO: Resolved: 0\n[2023-10-24 14:07:46] INFO: >>>STAGE: contigger\n[2023-10-24 14:07:46] INFO: Generating contigs\n[2023-10-24 14:07:46] INFO: Reading sequences\n[2023-10-24 14:07:46] INFO: Generated 1 contigs\n[2023-10-24 14:07:46] INFO: Added 0 scaffold connections\n[2023-10-24 14:07:46] INFO: >>>STAGE: polishing\n[2023-10-24 14:07:46] INFO: Polishing genome (1/1)\n[2023-10-24 14:07:46] INFO: Running minimap2\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a453b500000051'\n[2023-10-24 14:07:47] INFO: Separating alignment into bubbles\n[2023-10-24 14:07:48] INFO: Alignment error rate: 0.104939\n[2023-10-24 14:07:48] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a453cc00000052'\n[2023-10-24 14:07:51] INFO: >>>STAGE: finalize\n[2023-10-24 14:07:51] INFO: Assembly statistics:\n\n\tTotal length:\t40419\n\tFragments:\t1\n\tFragments N50:\t40419\n\tLargest frg:\t40419\n\tScaffolds:\t0\n\tMean coverage:\t26\n\n[2023-10-24 14:07:51] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/76/working/out_dir/assembly.fasta\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "104.0000000"}, {"title": "Job End Time", "value": "2023-10-24 14:07:51", "plugin": "core", "name": "end_epoch", "raw_value": "1698156471.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:06:07", "plugin": "core", "name": "start_epoch", "raw_value": "1698156367.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "flye/2.6-2", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.6", "test_index": 2, "time_seconds": 234.7394893169403, "inputs": {"inputs": {"src": "hda", "id": "69a9a813088bd0f8"}, "mode": "--nano-corr", "g": "10000", "i": "2", "asm": "40"}, "job": {"model_class": "Job", "id": "54e969cd1cecc0e7", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:11:55.315153", "create_time": "2023-10-24T14:08:13.813198", "galaxy_version": "21.09", "command_version": "2.6-release", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6", "history_id": "639c57257ba4f009", "external_id": "gxy-m7h4r", "command_line": "ln -s '/galaxy/server/database/objects/9/d/9/dataset_9d97eac8-24cd-4dc3-8881-1187e7be2a29.dat' ./input_0.fasta && flye --nano-corr ./input_0.fasta -o out_dir -g '10000' -t ${GALAXY_SLOTS:-4} -i 2 --asm-coverage '40' 2>&1", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "no_trestle": "\"false\"", "meta": "\"false\"", "plasmids": "\"false\"", "asm": "\"40\"", "m": "\"\"", "i": "\"2\"", "g": "\"10000\"", "mode": "\"--nano-corr\""}, "inputs": {"inputs": {"id": "69a9a813088bd0f8", "src": "hda", "uuid": "9d97eac8-24cd-4dc3-8881-1187e7be2a29"}}, "outputs": {"consensus": {"id": "87d277e0196a2c42", "src": "hda", "uuid": "03a9c2cf-f04d-42e8-9712-e5cf045ef20d"}, "assembly_graph": {"id": "1ad10c8dbe64ac9d", "src": "hda", "uuid": "4179d729-cb80-43c1-a48b-595d4cadcfc4"}, "assembly_gfa": {"id": "0813abae44372405", "src": "hda", "uuid": "32305289-08e0-49dd-8573-b39f75e80366"}, "assembly_info": {"id": "2494fbd0def70806", "src": "hda", "uuid": "88363d6c-f03d-4855-a94b-ac4ef66b99a9"}, "flye_log": {"id": "68e9974f5915fb94", "src": "hda", "uuid": "b0a0ef91-69b8-44cb-bebf-2e19dfc0a0d3"}}, "output_collections": {}, "tool_stdout": "[2023-10-24 14:10:04] INFO: Starting Flye 2.6-release\n[2023-10-24 14:10:04] INFO: >>>STAGE: configure\n[2023-10-24 14:10:04] INFO: Configuring run\n[2023-10-24 14:10:04] INFO: Total read length: 1466260\n[2023-10-24 14:10:04] INFO: Input genome size: 10000\n[2023-10-24 14:10:04] INFO: Estimated coverage: 146\n[2023-10-24 14:10:04] INFO: Reads N50/N90: 9054 / 4697\n[2023-10-24 14:10:04] INFO: Minimum overlap set to 5000\n[2023-10-24 14:10:04] INFO: Selected k-mer size: 17\n[2023-10-24 14:10:04] INFO: Using longest 40x reads for contig assembly\n[2023-10-24 14:10:04] INFO: >>>STAGE: assembly\n[2023-10-24 14:10:04] INFO: Assembling disjointigs\n[2023-10-24 14:10:04] INFO: Reading sequences\n[2023-10-24 14:10:04] INFO: Generating solid k-mer index\n[2023-10-24 14:10:26] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:10:26] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:10:26] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:10:48] INFO: Extending reads\n[2023-10-24 14:10:48] INFO: Overlap-based coverage: 3\n[2023-10-24 14:10:48] INFO: Median overlap divergence: 0.173521\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:10:48] INFO: Assembled 1 disjointigs\n[2023-10-24 14:10:48] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2023-10-24 14:10:49] INFO: >>>STAGE: consensus\n[2023-10-24 14:10:49] INFO: Running Minimap2\n[2023-10-24 14:10:50] INFO: Computing consensus\n[2023-10-24 14:10:51] INFO: Alignment error rate: 0.146313\n[2023-10-24 14:10:51] INFO: >>>STAGE: repeat\n[2023-10-24 14:10:51] INFO: Building and resolving repeat graph\n[2023-10-24 14:10:51] INFO: Reading sequences\n[2023-10-24 14:10:51] INFO: Building repeat graph\n50% 100% \n[2023-10-24 14:11:13] INFO: Median overlap divergence: 0\n[2023-10-24 14:11:13] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:11:36] INFO: Aligned read sequence: 1174263 / 1313105 (0.894264)\n[2023-10-24 14:11:36] INFO: Median overlap divergence: 0.0589391\n[2023-10-24 14:11:36] INFO: Mean edge coverage: 29\n[2023-10-24 14:11:36] INFO: Resolving repeats\n[2023-10-24 14:11:36] INFO: >>>STAGE: contigger\n[2023-10-24 14:11:36] INFO: Generating contigs\n[2023-10-24 14:11:36] INFO: Reading sequences\n[2023-10-24 14:11:36] INFO: Generated 1 contigs\n[2023-10-24 14:11:36] INFO: Added 0 scaffold connections\n[2023-10-24 14:11:36] INFO: >>>STAGE: polishing\n[2023-10-24 14:11:36] INFO: Polishing genome (1/2)\n[2023-10-24 14:11:36] INFO: Running minimap2\n[2023-10-24 14:11:37] INFO: Separating alignment into bubbles\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a453fc00000056'\n[2023-10-24 14:11:38] INFO: Alignment error rate: 0.099017\n[2023-10-24 14:11:38] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a4540e00000057'\n[2023-10-24 14:11:41] INFO: Polishing genome (2/2)\n[2023-10-24 14:11:41] INFO: Running minimap2\n[2023-10-24 14:11:41] INFO: Separating alignment into bubbles\n[2023-10-24 14:11:42] INFO: Alignment error rate: 0.094400\n[2023-10-24 14:11:42] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:11:45] INFO: >>>STAGE: finalize\n[2023-10-24 14:11:45] INFO: Assembly statistics:\n\n\tTotal length:\t40414\n\tFragments:\t1\n\tFragments N50:\t40414\n\tLargest frg:\t40414\n\tScaffolds:\t0\n\tMean coverage:\t27\n\n[2023-10-24 14:11:45] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/78/working/out_dir/assembly.fasta\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a4540f00000059'\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "[2023-10-24 14:10:04] INFO: Starting Flye 2.6-release\n[2023-10-24 14:10:04] INFO: >>>STAGE: configure\n[2023-10-24 14:10:04] INFO: Configuring run\n[2023-10-24 14:10:04] INFO: Total read length: 1466260\n[2023-10-24 14:10:04] INFO: Input genome size: 10000\n[2023-10-24 14:10:04] INFO: Estimated coverage: 146\n[2023-10-24 14:10:04] INFO: Reads N50/N90: 9054 / 4697\n[2023-10-24 14:10:04] INFO: Minimum overlap set to 5000\n[2023-10-24 14:10:04] INFO: Selected k-mer size: 17\n[2023-10-24 14:10:04] INFO: Using longest 40x reads for contig assembly\n[2023-10-24 14:10:04] INFO: >>>STAGE: assembly\n[2023-10-24 14:10:04] INFO: Assembling disjointigs\n[2023-10-24 14:10:04] INFO: Reading sequences\n[2023-10-24 14:10:04] INFO: Generating solid k-mer index\n[2023-10-24 14:10:26] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:10:26] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:10:26] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:10:48] INFO: Extending reads\n[2023-10-24 14:10:48] INFO: Overlap-based coverage: 3\n[2023-10-24 14:10:48] INFO: Median overlap divergence: 0.173521\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:10:48] INFO: Assembled 1 disjointigs\n[2023-10-24 14:10:48] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2023-10-24 14:10:49] INFO: >>>STAGE: consensus\n[2023-10-24 14:10:49] INFO: Running Minimap2\n[2023-10-24 14:10:50] INFO: Computing consensus\n[2023-10-24 14:10:51] INFO: Alignment error rate: 0.146313\n[2023-10-24 14:10:51] INFO: >>>STAGE: repeat\n[2023-10-24 14:10:51] INFO: Building and resolving repeat graph\n[2023-10-24 14:10:51] INFO: Reading sequences\n[2023-10-24 14:10:51] INFO: Building repeat graph\n50% 100% \n[2023-10-24 14:11:13] INFO: Median overlap divergence: 0\n[2023-10-24 14:11:13] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:11:36] INFO: Aligned read sequence: 1174263 / 1313105 (0.894264)\n[2023-10-24 14:11:36] INFO: Median overlap divergence: 0.0589391\n[2023-10-24 14:11:36] INFO: Mean edge coverage: 29\n[2023-10-24 14:11:36] INFO: Resolving repeats\n[2023-10-24 14:11:36] INFO: >>>STAGE: contigger\n[2023-10-24 14:11:36] INFO: Generating contigs\n[2023-10-24 14:11:36] INFO: Reading sequences\n[2023-10-24 14:11:36] INFO: Generated 1 contigs\n[2023-10-24 14:11:36] INFO: Added 0 scaffold connections\n[2023-10-24 14:11:36] INFO: >>>STAGE: polishing\n[2023-10-24 14:11:36] INFO: Polishing genome (1/2)\n[2023-10-24 14:11:36] INFO: Running minimap2\n[2023-10-24 14:11:37] INFO: Separating alignment into bubbles\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a453fc00000056'\n[2023-10-24 14:11:38] INFO: Alignment error rate: 0.099017\n[2023-10-24 14:11:38] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a4540e00000057'\n[2023-10-24 14:11:41] INFO: Polishing genome (2/2)\n[2023-10-24 14:11:41] INFO: Running minimap2\n[2023-10-24 14:11:41] INFO: Separating alignment into bubbles\n[2023-10-24 14:11:42] INFO: Alignment error rate: 0.094400\n[2023-10-24 14:11:42] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:11:45] INFO: >>>STAGE: finalize\n[2023-10-24 14:11:45] INFO: Assembly statistics:\n\n\tTotal length:\t40414\n\tFragments:\t1\n\tFragments N50:\t40414\n\tLargest frg:\t40414\n\tScaffolds:\t0\n\tMean coverage:\t27\n\n[2023-10-24 14:11:45] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/78/working/out_dir/assembly.fasta\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a4540f00000059'\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "101.0000000"}, {"title": "Job End Time", "value": "2023-10-24 14:11:45", "plugin": "core", "name": "end_epoch", "raw_value": "1698156705.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:10:04", "plugin": "core", "name": "start_epoch", "raw_value": "1698156604.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "flye/2.6-3", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.6", "test_index": 3, "time_seconds": 237.4103660583496, "inputs": {"inputs": {"src": "hda", "id": "94619fc465ac7c18"}, "mode": "--pacbio-raw", "g": "10000", "i": "1", "plasmids": true, "meta": true}, "job": {"model_class": "Job", "id": "71a8d024bd56e8a0", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:15:52.805564", "create_time": "2023-10-24T14:12:08.728591", "galaxy_version": "21.09", "command_version": "2.6-release", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6", "history_id": "639c57257ba4f009", "external_id": "gxy-hkqch", "command_line": "ln -s '/galaxy/server/database/objects/4/7/5/dataset_475e9eec-20f0-40bf-9a6e-9e8ebac7426f.dat' ./input_0.fasta && flye --pacbio-raw ./input_0.fasta -o out_dir -g '10000' -t ${GALAXY_SLOTS:-4} -i 1 --plasmids --meta 2>&1", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "no_trestle": "\"false\"", "meta": "\"true\"", "plasmids": "\"true\"", "asm": "\"\"", "m": "\"\"", "i": "\"1\"", "g": "\"10000\"", "mode": "\"--pacbio-raw\""}, "inputs": {"inputs": {"id": "94619fc465ac7c18", "src": "hda", "uuid": "475e9eec-20f0-40bf-9a6e-9e8ebac7426f"}}, "outputs": {"consensus": {"id": "b2ba8230d015ae40", "src": "hda", "uuid": "dd4bac1b-44f7-46c6-933a-2ad5cfdaee53"}, "assembly_graph": {"id": "e06f785986a67751", "src": "hda", "uuid": "5b1a8762-94c5-4fdd-8e29-62dcfddd2991"}, "assembly_gfa": {"id": "5bf13881de2cb9fb", "src": "hda", "uuid": "4f481af0-d2f2-47c3-ad89-3f6d41c0769e"}, "assembly_info": {"id": "00e58e0d5093fb1c", "src": "hda", "uuid": "7c3bf156-6d47-4617-8302-6c05d3f1927f"}, "flye_log": {"id": "0ec8b65e7fdd167e", "src": "hda", "uuid": "ed1c2931-9cf2-40ad-bed4-183a0708f438"}}, "output_collections": {}, "tool_stdout": "[2023-10-24 14:13:56] INFO: Starting Flye 2.6-release\n[2023-10-24 14:13:56] INFO: >>>STAGE: configure\n[2023-10-24 14:13:56] INFO: Configuring run\n[2023-10-24 14:13:56] INFO: Total read length: 1466260\n[2023-10-24 14:13:56] INFO: Input genome size: 10000\n[2023-10-24 14:13:56] INFO: Estimated coverage: 146\n[2023-10-24 14:13:56] INFO: Reads N50/N90: 9054 / 4697\n[2023-10-24 14:13:56] INFO: Minimum overlap set to 5000\n[2023-10-24 14:13:56] INFO: Selected k-mer size: 15\n[2023-10-24 14:13:56] INFO: >>>STAGE: assembly\n[2023-10-24 14:13:56] INFO: Assembling disjointigs\n[2023-10-24 14:13:56] INFO: Reading sequences\n[2023-10-24 14:13:56] INFO: Generating solid k-mer index\n[2023-10-24 14:14:18] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:14:18] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:14:18] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:14:19] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:14:43] INFO: Extending reads\n[2023-10-24 14:14:46] INFO: Overlap-based coverage: 24\n[2023-10-24 14:14:46] INFO: Median overlap divergence: 0.184187\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:14:47] INFO: Assembled 1 disjointigs\n[2023-10-24 14:14:47] INFO: Generating sequence\n10% 20% 30% 40% 50% 60% 70% 80% 100% \n[2023-10-24 14:14:49] INFO: >>>STAGE: consensus\n[2023-10-24 14:14:49] INFO: Running Minimap2\n[2023-10-24 14:14:50] INFO: Computing consensus\n[2023-10-24 14:14:51] INFO: Alignment error rate: 0.183209\n[2023-10-24 14:14:51] INFO: >>>STAGE: repeat\n[2023-10-24 14:14:51] INFO: Building and resolving repeat graph\n[2023-10-24 14:14:51] INFO: Reading sequences\n[2023-10-24 14:14:51] INFO: Building repeat graph\n50% 100% \n[2023-10-24 14:15:13] INFO: Median overlap divergence: 0\n[2023-10-24 14:15:13] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:15:36] INFO: Aligned read sequence: 1158698 / 1313105 (0.882411)\n[2023-10-24 14:15:36] INFO: Median overlap divergence: 0.0642069\n[2023-10-24 14:15:36] INFO: Mean edge coverage: 32\n[2023-10-24 14:15:36] INFO: Resolving repeats\n[2023-10-24 14:15:36] INFO: >>>STAGE: plasmids\n[2023-10-24 14:15:36] INFO: Recovering short unassembled sequences\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a4543c0000005d'\n[2023-10-24 14:15:36] INFO: Added 0 extra contigs\n[2023-10-24 14:15:36] INFO: >>>STAGE: contigger\n[2023-10-24 14:15:36] INFO: Generating contigs\n[2023-10-24 14:15:36] INFO: Reading sequences\n[2023-10-24 14:15:36] INFO: Generated 1 contigs\n[2023-10-24 14:15:36] INFO: Added 0 scaffold connections\n[2023-10-24 14:15:36] INFO: >>>STAGE: polishing\n[2023-10-24 14:15:36] INFO: Polishing genome (1/1)\n[2023-10-24 14:15:36] INFO: Running minimap2\n[2023-10-24 14:15:37] INFO: Separating alignment into bubbles\n[2023-10-24 14:15:38] INFO: Alignment error rate: 0.115105\n[2023-10-24 14:15:38] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a4544c0000005e'\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a454580000005f'\n[2023-10-24 14:15:42] INFO: >>>STAGE: finalize\n[2023-10-24 14:15:42] INFO: Assembly statistics:\n\n\tTotal length:\t35685\n\tFragments:\t1\n\tFragments N50:\t35685\n\tLargest frg:\t35685\n\tScaffolds:\t0\n\tMean coverage:\t36\n\n[2023-10-24 14:15:42] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/80/working/out_dir/assembly.fasta\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "[2023-10-24 14:13:56] INFO: Starting Flye 2.6-release\n[2023-10-24 14:13:56] INFO: >>>STAGE: configure\n[2023-10-24 14:13:56] INFO: Configuring run\n[2023-10-24 14:13:56] INFO: Total read length: 1466260\n[2023-10-24 14:13:56] INFO: Input genome size: 10000\n[2023-10-24 14:13:56] INFO: Estimated coverage: 146\n[2023-10-24 14:13:56] INFO: Reads N50/N90: 9054 / 4697\n[2023-10-24 14:13:56] INFO: Minimum overlap set to 5000\n[2023-10-24 14:13:56] INFO: Selected k-mer size: 15\n[2023-10-24 14:13:56] INFO: >>>STAGE: assembly\n[2023-10-24 14:13:56] INFO: Assembling disjointigs\n[2023-10-24 14:13:56] INFO: Reading sequences\n[2023-10-24 14:13:56] INFO: Generating solid k-mer index\n[2023-10-24 14:14:18] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:14:18] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:14:18] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:14:19] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:14:43] INFO: Extending reads\n[2023-10-24 14:14:46] INFO: Overlap-based coverage: 24\n[2023-10-24 14:14:46] INFO: Median overlap divergence: 0.184187\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:14:47] INFO: Assembled 1 disjointigs\n[2023-10-24 14:14:47] INFO: Generating sequence\n10% 20% 30% 40% 50% 60% 70% 80% 100% \n[2023-10-24 14:14:49] INFO: >>>STAGE: consensus\n[2023-10-24 14:14:49] INFO: Running Minimap2\n[2023-10-24 14:14:50] INFO: Computing consensus\n[2023-10-24 14:14:51] INFO: Alignment error rate: 0.183209\n[2023-10-24 14:14:51] INFO: >>>STAGE: repeat\n[2023-10-24 14:14:51] INFO: Building and resolving repeat graph\n[2023-10-24 14:14:51] INFO: Reading sequences\n[2023-10-24 14:14:51] INFO: Building repeat graph\n50% 100% \n[2023-10-24 14:15:13] INFO: Median overlap divergence: 0\n[2023-10-24 14:15:13] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2023-10-24 14:15:36] INFO: Aligned read sequence: 1158698 / 1313105 (0.882411)\n[2023-10-24 14:15:36] INFO: Median overlap divergence: 0.0642069\n[2023-10-24 14:15:36] INFO: Mean edge coverage: 32\n[2023-10-24 14:15:36] INFO: Resolving repeats\n[2023-10-24 14:15:36] INFO: >>>STAGE: plasmids\n[2023-10-24 14:15:36] INFO: Recovering short unassembled sequences\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a4543c0000005d'\n[2023-10-24 14:15:36] INFO: Added 0 extra contigs\n[2023-10-24 14:15:36] INFO: >>>STAGE: contigger\n[2023-10-24 14:15:36] INFO: Generating contigs\n[2023-10-24 14:15:36] INFO: Reading sequences\n[2023-10-24 14:15:36] INFO: Generated 1 contigs\n[2023-10-24 14:15:36] INFO: Added 0 scaffold connections\n[2023-10-24 14:15:36] INFO: >>>STAGE: polishing\n[2023-10-24 14:15:36] INFO: Polishing genome (1/1)\n[2023-10-24 14:15:36] INFO: Running minimap2\n[2023-10-24 14:15:37] INFO: Separating alignment into bubbles\n[2023-10-24 14:15:38] INFO: Alignment error rate: 0.115105\n[2023-10-24 14:15:38] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a4544c0000005e'\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000a454580000005f'\n[2023-10-24 14:15:42] INFO: >>>STAGE: finalize\n[2023-10-24 14:15:42] INFO: Assembly statistics:\n\n\tTotal length:\t35685\n\tFragments:\t1\n\tFragments N50:\t35685\n\tLargest frg:\t35685\n\tScaffolds:\t0\n\tMean coverage:\t36\n\n[2023-10-24 14:15:42] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/80/working/out_dir/assembly.fasta\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "107.0000000"}, {"title": "Job End Time", "value": "2023-10-24 14:15:42", "plugin": "core", "name": "end_epoch", "raw_value": "1698156942.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:13:55", "plugin": "core", "name": "start_epoch", "raw_value": "1698156835.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-0", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 0, "time_seconds": 143.73372769355774, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "58512eaacbf9db4c"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "413de22edc62375f"}, "library|input_2": {"src": "hda", "id": "899e08e1b441ec18"}, "library|type": "paired", "adv|reporting_options|reporting_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "51c25f1caa684f9b", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:49:24.211618", "create_time": "2023-10-24T14:47:16.034987", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-jqzw9", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/0/2/6/dataset_0261fbbe-785c-49f7-afb4-2b7f2ae756e7.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/a/0/c/dataset_a0c4f8ab-c303-422f-bf7c-ec2ea3aa4061.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/7/d/e/dataset_7de913b1-e670-4800-a59a-7eaf6ece5320.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/f/0/8/dataset_f08f19d9-ca43-428c-9b0c-129eb387ff7b.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 1, \"max_primary\": \"\", \"reporting_options_selector\": \"advanced\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 178, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 179, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 177, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "58512eaacbf9db4c", "src": "hda", "uuid": "0261fbbe-785c-49f7-afb4-2b7f2ae756e7"}, "input_1": {"id": "413de22edc62375f", "src": "hda", "uuid": "a0c4f8ab-c303-422f-bf7c-ec2ea3aa4061"}, "input_2": {"id": "899e08e1b441ec18", "src": "hda", "uuid": "7de913b1-e670-4800-a59a-7eaf6ece5320"}}, "outputs": {"output_alignments": {"id": "4cd1e2380ea36dc1", "src": "hda", "uuid": "f08f19d9-ca43-428c-9b0c-129eb387ff7b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\n Reserving size (252) for bucket 2\nGetting block 3 of 29\n Calculating Z arrays for bucket 2\n Reserving size (252) for bucket 3\n Entering block accumulator loop for bucket 1:\nGetting block 4 of 29\n Calculating Z arrays for bucket 3\n Reserving size (252) for bucket 4\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 4\n bucket 1: 10%\n bucket 2: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 3:\n bucket 2: 20%\n Entering block accumulator loop for bucket 4:\n bucket 1: 30%\n bucket 2: 30%\n bucket 3: 10%\n bucket 1: 40%\n bucket 2: 40%\n bucket 4: 10%\n bucket 1: 50%\n bucket 3: 20%\n bucket 2: 50%\n bucket 1: 60%\n bucket 4: 20%\n bucket 3: 30%\n bucket 2: 60%\n bucket 1: 70%\n bucket 4: 30%\n bucket 3: 40%\n bucket 2: 70%\n bucket 1: 80%\n bucket 4: 40%\n bucket 3: 50%\n bucket 1: 90%\n bucket 2: 80%\n bucket 4: 50%\n bucket 3: 60%\n bucket 2: 90%\n bucket 4: 60%\n bucket 1: 100%\n bucket 3: 70%\n bucket 2: 100%\n Sorting block of length 127 for bucket 1\n Sorting block of length 239 for bucket 2\n bucket 3: 80%\n (Using difference cover)\n bucket 4: 70%\n bucket 3: 90%\n bucket 4: 80%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n bucket 4: 90%\n (Using difference cover)\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\nGetting block 5 of 29\nGetting block 6 of 29\n Reserving size (252) for bucket 5\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n Entering block accumulator loop for bucket 6:\n bucket 5: 20%\n bucket 5: 30%\n bucket 6: 10%\n bucket 5: 40%\n bucket 6: 20%\n bucket 5: 50%\n bucket 6: 30%\n bucket 5: 60%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 5: 70%\n bucket 6: 80%\n bucket 5: 80%\n bucket 6: 90%\n bucket 5: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\nGetting block 7 of 29\nGetting block 8 of 29\n Reserving size (252) for bucket 7\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 7:\n bucket 8: 10%\n bucket 7: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 7: 20%\n bucket 8: 50%\n bucket 7: 30%\n bucket 8: 60%\n bucket 7: 40%\n bucket 8: 70%\n bucket 7: 50%\n bucket 8: 80%\n bucket 7: 60%\n bucket 8: 90%\n bucket 7: 70%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n bucket 7: 80%\n (Using difference cover)\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 9: 50%\n bucket 10: 50%\n bucket 9: 60%\n bucket 10: 60%\n bucket 9: 70%\n bucket 10: 70%\n bucket 9: 80%\n bucket 10: 80%\n bucket 9: 90%\n bucket 10: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 12:\n bucket 11: 10%\n bucket 12: 10%\n bucket 12: 20%\n bucket 11: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 11: 30%\n bucket 12: 50%\n bucket 11: 40%\n bucket 12: 60%\n bucket 11: 50%\n bucket 12: 70%\n bucket 11: 60%\n bucket 12: 80%\n bucket 12: 90%\n bucket 11: 70%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n bucket 11: 80%\n bucket 11: 90%\n (Using difference cover)\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 70%\n bucket 13: 80%\n Entering block accumulator loop for bucket 14:\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n bucket 14: 10%\n (Using difference cover)\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 17\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 18: 10%\n bucket 17: 20%\n bucket 18: 20%\n bucket 17: 30%\n bucket 18: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 18: 40%\n bucket 17: 80%\n bucket 18: 50%\n bucket 17: 90%\n bucket 18: 60%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n bucket 19: 100%\n Calculating Z arrays for bucket 20\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\nGetting block 22 of 29\n bucket 21: 60%\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 70%\n bucket 21: 80%\n Entering block accumulator loop for bucket 22:\n bucket 21: 90%\n bucket 21: 100%\n bucket 22: 10%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n bucket 23: 10%\n Calculating Z arrays for bucket 24\n bucket 23: 20%\n bucket 23: 30%\n Entering block accumulator loop for bucket 24:\n bucket 23: 40%\n bucket 23: 50%\n bucket 24: 10%\n bucket 23: 60%\n bucket 24: 20%\n bucket 23: 70%\n bucket 23: 80%\n bucket 24: 30%\n bucket 23: 90%\n bucket 24: 40%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\n Reserving size (252) for bucket 2\nGetting block 3 of 29\n Calculating Z arrays for bucket 2\n Reserving size (252) for bucket 3\n Entering block accumulator loop for bucket 1:\nGetting block 4 of 29\n Calculating Z arrays for bucket 3\n Reserving size (252) for bucket 4\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 4\n bucket 1: 10%\n bucket 2: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 3:\n bucket 2: 20%\n Entering block accumulator loop for bucket 4:\n bucket 1: 30%\n bucket 2: 30%\n bucket 3: 10%\n bucket 1: 40%\n bucket 2: 40%\n bucket 4: 10%\n bucket 1: 50%\n bucket 3: 20%\n bucket 2: 50%\n bucket 1: 60%\n bucket 4: 20%\n bucket 3: 30%\n bucket 2: 60%\n bucket 1: 70%\n bucket 4: 30%\n bucket 3: 40%\n bucket 2: 70%\n bucket 1: 80%\n bucket 4: 40%\n bucket 3: 50%\n bucket 1: 90%\n bucket 2: 80%\n bucket 4: 50%\n bucket 3: 60%\n bucket 2: 90%\n bucket 4: 60%\n bucket 1: 100%\n bucket 3: 70%\n bucket 2: 100%\n Sorting block of length 127 for bucket 1\n Sorting block of length 239 for bucket 2\n bucket 3: 80%\n (Using difference cover)\n bucket 4: 70%\n bucket 3: 90%\n bucket 4: 80%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n bucket 4: 90%\n (Using difference cover)\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\nGetting block 5 of 29\nGetting block 6 of 29\n Reserving size (252) for bucket 5\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n Entering block accumulator loop for bucket 6:\n bucket 5: 20%\n bucket 5: 30%\n bucket 6: 10%\n bucket 5: 40%\n bucket 6: 20%\n bucket 5: 50%\n bucket 6: 30%\n bucket 5: 60%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 5: 70%\n bucket 6: 80%\n bucket 5: 80%\n bucket 6: 90%\n bucket 5: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\nGetting block 7 of 29\nGetting block 8 of 29\n Reserving size (252) for bucket 7\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 7:\n bucket 8: 10%\n bucket 7: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 7: 20%\n bucket 8: 50%\n bucket 7: 30%\n bucket 8: 60%\n bucket 7: 40%\n bucket 8: 70%\n bucket 7: 50%\n bucket 8: 80%\n bucket 7: 60%\n bucket 8: 90%\n bucket 7: 70%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n bucket 7: 80%\n (Using difference cover)\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 9: 50%\n bucket 10: 50%\n bucket 9: 60%\n bucket 10: 60%\n bucket 9: 70%\n bucket 10: 70%\n bucket 9: 80%\n bucket 10: 80%\n bucket 9: 90%\n bucket 10: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 12:\n bucket 11: 10%\n bucket 12: 10%\n bucket 12: 20%\n bucket 11: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 11: 30%\n bucket 12: 50%\n bucket 11: 40%\n bucket 12: 60%\n bucket 11: 50%\n bucket 12: 70%\n bucket 11: 60%\n bucket 12: 80%\n bucket 12: 90%\n bucket 11: 70%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n bucket 11: 80%\n bucket 11: 90%\n (Using difference cover)\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 70%\n bucket 13: 80%\n Entering block accumulator loop for bucket 14:\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n bucket 14: 10%\n (Using difference cover)\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 17\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 18: 10%\n bucket 17: 20%\n bucket 18: 20%\n bucket 17: 30%\n bucket 18: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 18: 40%\n bucket 17: 80%\n bucket 18: 50%\n bucket 17: 90%\n bucket 18: 60%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n bucket 19: 100%\n Calculating Z arrays for bucket 20\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\nGetting block 22 of 29\n bucket 21: 60%\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 70%\n bucket 21: 80%\n Entering block accumulator loop for bucket 22:\n bucket 21: 90%\n bucket 21: 100%\n bucket 22: 10%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n bucket 23: 10%\n Calculating Z arrays for bucket 24\n bucket 23: 20%\n bucket 23: 30%\n Entering block accumulator loop for bucket 24:\n bucket 23: 40%\n bucket 23: 50%\n bucket 24: 10%\n bucket 23: 60%\n bucket 24: 20%\n bucket 23: 70%\n bucket 23: 80%\n bucket 24: 30%\n bucket 23: 90%\n bucket 24: 40%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "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": "2023-10-24 14:49:12", "plugin": "core", "name": "end_epoch", "raw_value": "1698158952.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:49:12", "plugin": "core", "name": "start_epoch", "raw_value": "1698158952.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-1", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 1, "time_seconds": 137.1554148197174, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "8d3138e601ba41cb"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "4f06b982641013af"}, "library|input_2": {"src": "hda", "id": "67393638607655c7"}, "library|type": "paired"}, "job": {"model_class": "Job", "id": "128787d8e2cf1a32", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:51:41.505425", "create_time": "2023-10-24T14:49:40.487374", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-c95c6", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/6/8/3/dataset_68380824-fdf7-47e5-8578-3512f9a62548.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/d/2/9/dataset_d292010a-cbe9-473f-9edd-26c807d49646.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/9/b/b/dataset_9bb996af-cdac-49f7-8d89-0c0160741fb6.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/a/3/f/dataset_a3ffbc4a-14b3-4699-a6f5-47aa8a0ec74a.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 182, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 183, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 181, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "8d3138e601ba41cb", "src": "hda", "uuid": "68380824-fdf7-47e5-8578-3512f9a62548"}, "input_1": {"id": "4f06b982641013af", "src": "hda", "uuid": "d292010a-cbe9-473f-9edd-26c807d49646"}, "input_2": {"id": "67393638607655c7", "src": "hda", "uuid": "9bb996af-cdac-49f7-8d89-0c0160741fb6"}}, "outputs": {"output_alignments": {"id": "5bfc253acb59ec31", "src": "hda", "uuid": "a3ffbc4a-14b3-4699-a6f5-47aa8a0ec74a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\nGetting block 2 of 29\n Reserving size (252) for bucket 1\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n Reserving size (252) for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n bucket 1: 10%\n Entering block accumulator loop for bucket 3:\nGetting block 4 of 29\n bucket 3: 10%\n Reserving size (252) for bucket 4\n bucket 2: 10%\n Calculating Z arrays for bucket 4\n bucket 3: 20%\n bucket 1: 20%\n bucket 2: 20%\n bucket 3: 30%\n bucket 1: 30%\n bucket 2: 30%\n bucket 3: 40%\n Entering block accumulator loop for bucket 4:\n bucket 1: 40%\n bucket 2: 40%\n bucket 1: 50%\n bucket 3: 50%\n bucket 2: 50%\n bucket 4: 10%\n bucket 1: 60%\n bucket 3: 60%\n bucket 2: 60%\n bucket 4: 20%\n bucket 1: 70%\n bucket 3: 70%\n bucket 2: 70%\n bucket 1: 80%\n bucket 3: 80%\n bucket 4: 30%\n bucket 2: 80%\n bucket 1: 90%\n bucket 3: 90%\n bucket 4: 40%\n bucket 2: 90%\n bucket 1: 100%\n bucket 3: 100%\n bucket 4: 50%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n Sorting block of length 166 for bucket 3\n bucket 4: 60%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n bucket 4: 70%\n bucket 4: 80%\n bucket 4: 90%\n (Using difference cover)\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n bucket 5: 100%\n Calculating Z arrays for bucket 6\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n Entering block accumulator loop for bucket 6:\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n bucket 9: 10%\n Calculating Z arrays for bucket 10\n bucket 9: 20%\n Entering block accumulator loop for bucket 10:\n bucket 9: 30%\n bucket 9: 40%\n bucket 10: 10%\n bucket 9: 50%\n bucket 10: 20%\n bucket 9: 60%\n bucket 10: 30%\n bucket 9: 70%\n bucket 10: 40%\n bucket 9: 80%\n bucket 10: 50%\n bucket 9: 90%\n bucket 10: 60%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 80%\n bucket 13: 90%\n Entering block accumulator loop for bucket 14:\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\nGetting block 18 of 29\n Sorting block time: 00:00:00\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\nReturning block of 163 for bucket 17\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 21\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 20:\n bucket 21: 10%\n bucket 21: 20%\n bucket 20: 10%\n bucket 21: 30%\n bucket 20: 20%\n bucket 21: 40%\n bucket 21: 50%\n bucket 20: 30%\n bucket 21: 60%\n bucket 20: 40%\n bucket 21: 70%\n bucket 21: 80%\n bucket 20: 50%\n bucket 21: 90%\n bucket 20: 60%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\nGetting block 25 of 29\n bucket 24: 10%\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 20%\n Entering block accumulator loop for bucket 25:\n bucket 24: 30%\n bucket 25: 10%\n bucket 24: 40%\n bucket 25: 20%\n bucket 24: 50%\n bucket 25: 30%\n bucket 25: 40%\n bucket 24: 60%\n bucket 25: 50%\n bucket 24: 70%\n bucket 25: 60%\n bucket 25: 70%\n bucket 24: 80%\n bucket 25: 80%\n bucket 25: 90%\n bucket 24: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n bucket 27: 30%\n Calculating Z arrays for bucket 28\n bucket 27: 40%\n bucket 27: 50%\n Entering block accumulator loop for bucket 28:\n bucket 27: 60%\n bucket 27: 70%\n bucket 28: 10%\n bucket 27: 80%\n bucket 28: 20%\n bucket 27: 90%\n bucket 28: 30%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\nGetting block 2 of 29\n Reserving size (252) for bucket 1\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n Reserving size (252) for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n bucket 1: 10%\n Entering block accumulator loop for bucket 3:\nGetting block 4 of 29\n bucket 3: 10%\n Reserving size (252) for bucket 4\n bucket 2: 10%\n Calculating Z arrays for bucket 4\n bucket 3: 20%\n bucket 1: 20%\n bucket 2: 20%\n bucket 3: 30%\n bucket 1: 30%\n bucket 2: 30%\n bucket 3: 40%\n Entering block accumulator loop for bucket 4:\n bucket 1: 40%\n bucket 2: 40%\n bucket 1: 50%\n bucket 3: 50%\n bucket 2: 50%\n bucket 4: 10%\n bucket 1: 60%\n bucket 3: 60%\n bucket 2: 60%\n bucket 4: 20%\n bucket 1: 70%\n bucket 3: 70%\n bucket 2: 70%\n bucket 1: 80%\n bucket 3: 80%\n bucket 4: 30%\n bucket 2: 80%\n bucket 1: 90%\n bucket 3: 90%\n bucket 4: 40%\n bucket 2: 90%\n bucket 1: 100%\n bucket 3: 100%\n bucket 4: 50%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n Sorting block of length 166 for bucket 3\n bucket 4: 60%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n bucket 4: 70%\n bucket 4: 80%\n bucket 4: 90%\n (Using difference cover)\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n bucket 5: 100%\n Calculating Z arrays for bucket 6\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n Entering block accumulator loop for bucket 6:\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n bucket 9: 10%\n Calculating Z arrays for bucket 10\n bucket 9: 20%\n Entering block accumulator loop for bucket 10:\n bucket 9: 30%\n bucket 9: 40%\n bucket 10: 10%\n bucket 9: 50%\n bucket 10: 20%\n bucket 9: 60%\n bucket 10: 30%\n bucket 9: 70%\n bucket 10: 40%\n bucket 9: 80%\n bucket 10: 50%\n bucket 9: 90%\n bucket 10: 60%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 80%\n bucket 13: 90%\n Entering block accumulator loop for bucket 14:\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\nGetting block 18 of 29\n Sorting block time: 00:00:00\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\nReturning block of 163 for bucket 17\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 21\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 20:\n bucket 21: 10%\n bucket 21: 20%\n bucket 20: 10%\n bucket 21: 30%\n bucket 20: 20%\n bucket 21: 40%\n bucket 21: 50%\n bucket 20: 30%\n bucket 21: 60%\n bucket 20: 40%\n bucket 21: 70%\n bucket 21: 80%\n bucket 20: 50%\n bucket 21: 90%\n bucket 20: 60%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\nGetting block 25 of 29\n bucket 24: 10%\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 20%\n Entering block accumulator loop for bucket 25:\n bucket 24: 30%\n bucket 25: 10%\n bucket 24: 40%\n bucket 25: 20%\n bucket 24: 50%\n bucket 25: 30%\n bucket 25: 40%\n bucket 24: 60%\n bucket 25: 50%\n bucket 24: 70%\n bucket 25: 60%\n bucket 25: 70%\n bucket 24: 80%\n bucket 25: 80%\n bucket 25: 90%\n bucket 24: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n bucket 27: 30%\n Calculating Z arrays for bucket 28\n bucket 27: 40%\n bucket 27: 50%\n Entering block accumulator loop for bucket 28:\n bucket 27: 60%\n bucket 27: 70%\n bucket 28: 10%\n bucket 27: 80%\n bucket 28: 20%\n bucket 27: 90%\n bucket 28: 30%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "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": "2023-10-24 14:51:31", "plugin": "core", "name": "end_epoch", "raw_value": "1698159091.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:51:31", "plugin": "core", "name": "start_epoch", "raw_value": "1698159091.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-10", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 10, "time_seconds": 135.29629778862, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "89a5e0f3eb2379c2"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "cb2f69b3f4b4b0b7"}, "library|rna_strandness": "R", "library|type": "single", "sum|new_summary": true, "sum|summary_file": true}, "job": {"model_class": "Job", "id": "d44e60ac329a0b36", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:12:30.791003", "create_time": "2023-10-24T15:10:27.718887", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-4bwsg", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/9/5/a/dataset_95a7f9bc-96f8-47f6-86dc-69e8fa8d62c7.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/0/1/a/dataset_01a6fa99-41c0-4871-81f4-0bcd3c3bb356.dat' input_f.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -U 'input_f.fastq' --rna-strandness R --new-summary --summary-file summary.txt | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/4/9/2/dataset_492555fb-84d7-4997-86dd-dd70ea4d98f9.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"true\", \"summary_file\": \"true\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 220, \"src\": \"hda\"}]}, \"rna_strandness\": \"R\", \"type\": \"single\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 219, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "89a5e0f3eb2379c2", "src": "hda", "uuid": "95a7f9bc-96f8-47f6-86dc-69e8fa8d62c7"}, "input_1": {"id": "cb2f69b3f4b4b0b7", "src": "hda", "uuid": "01a6fa99-41c0-4871-81f4-0bcd3c3bb356"}}, "outputs": {"output_alignments": {"id": "17e41ae056b859ea", "src": "hda", "uuid": "492555fb-84d7-4997-86dd-dd70ea4d98f9"}, "summary_file": {"id": "d0b87c6bbc602e9c", "src": "hda", "uuid": "ee93c01f-ca5f-43b9-98c1-f78fe1e29da8"}}, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\n Entering block accumulator loop for bucket 1:\n Reserving size (252) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n bucket 1: 20%\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n bucket 1: 40%\n Entering block accumulator loop for bucket 3:\n bucket 2: 10%\n bucket 1: 50%\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n bucket 2: 20%\n bucket 3: 10%\n bucket 1: 60%\n Calculating Z arrays for bucket 4\n bucket 2: 30%\n bucket 1: 70%\n bucket 3: 20%\n bucket 2: 40%\n bucket 1: 80%\n bucket 3: 30%\n Entering block accumulator loop for bucket 4:\n bucket 2: 50%\n bucket 1: 90%\n bucket 3: 40%\n bucket 4: 10%\n bucket 1: 100%\n bucket 2: 60%\n bucket 3: 50%\n bucket 4: 20%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 3: 60%\n bucket 4: 30%\n bucket 2: 70%\n bucket 3: 70%\n bucket 4: 40%\n bucket 2: 80%\n bucket 3: 80%\n bucket 4: 50%\n bucket 2: 90%\n bucket 3: 90%\n bucket 4: 60%\n bucket 2: 100%\n bucket 3: 100%\n bucket 4: 70%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 4: 80%\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\nGetting block 6 of 29\n bucket 5: 80%\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\nGetting block 7 of 29\n Entering block accumulator loop for bucket 6:\n Reserving size (252) for bucket 7\n bucket 5: 90%\n Calculating Z arrays for bucket 7\n bucket 6: 10%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 20%\n Entering block accumulator loop for bucket 7:\n bucket 6: 30%\n bucket 7: 10%\n bucket 6: 40%\n bucket 7: 20%\n bucket 6: 50%\n bucket 7: 30%\n bucket 6: 60%\n bucket 7: 40%\n bucket 6: 70%\n bucket 7: 50%\n bucket 7: 60%\n bucket 6: 80%\n bucket 7: 70%\n bucket 6: 90%\n bucket 7: 80%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 11\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 11: 10%\n bucket 12: 20%\n bucket 11: 20%\n bucket 12: 30%\n bucket 11: 30%\n bucket 12: 40%\n bucket 11: 40%\n bucket 12: 50%\n bucket 11: 50%\n bucket 12: 60%\n bucket 11: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 29\n Entering block accumulator loop for bucket 13:\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 10%\n Entering block accumulator loop for bucket 14:\n bucket 13: 20%\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 14: 60%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\nHISAT2 summary stats:\n\tTotal reads: 10\n\t\tAligned 0 time: 0 (0.00%)\n\t\tAligned 1 time: 10 (100.00%)\n\t\tAligned >1 times: 0 (0.00%)\n\tOverall alignment rate: 100.00%\n", "job_stdout": "", "job_stderr": "", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\nHISAT2 summary stats:\n\tTotal reads: 10\n\t\tAligned 0 time: 0 (0.00%)\n\t\tAligned 1 time: 10 (100.00%)\n\t\tAligned >1 times: 0 (0.00%)\n\tOverall alignment rate: 100.00%\n", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\n Entering block accumulator loop for bucket 1:\n Reserving size (252) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n bucket 1: 20%\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n bucket 1: 40%\n Entering block accumulator loop for bucket 3:\n bucket 2: 10%\n bucket 1: 50%\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n bucket 2: 20%\n bucket 3: 10%\n bucket 1: 60%\n Calculating Z arrays for bucket 4\n bucket 2: 30%\n bucket 1: 70%\n bucket 3: 20%\n bucket 2: 40%\n bucket 1: 80%\n bucket 3: 30%\n Entering block accumulator loop for bucket 4:\n bucket 2: 50%\n bucket 1: 90%\n bucket 3: 40%\n bucket 4: 10%\n bucket 1: 100%\n bucket 2: 60%\n bucket 3: 50%\n bucket 4: 20%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 3: 60%\n bucket 4: 30%\n bucket 2: 70%\n bucket 3: 70%\n bucket 4: 40%\n bucket 2: 80%\n bucket 3: 80%\n bucket 4: 50%\n bucket 2: 90%\n bucket 3: 90%\n bucket 4: 60%\n bucket 2: 100%\n bucket 3: 100%\n bucket 4: 70%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 4: 80%\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\nGetting block 6 of 29\n bucket 5: 80%\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\nGetting block 7 of 29\n Entering block accumulator loop for bucket 6:\n Reserving size (252) for bucket 7\n bucket 5: 90%\n Calculating Z arrays for bucket 7\n bucket 6: 10%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 20%\n Entering block accumulator loop for bucket 7:\n bucket 6: 30%\n bucket 7: 10%\n bucket 6: 40%\n bucket 7: 20%\n bucket 6: 50%\n bucket 7: 30%\n bucket 6: 60%\n bucket 7: 40%\n bucket 6: 70%\n bucket 7: 50%\n bucket 7: 60%\n bucket 6: 80%\n bucket 7: 70%\n bucket 6: 90%\n bucket 7: 80%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 11\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 11: 10%\n bucket 12: 20%\n bucket 11: 20%\n bucket 12: 30%\n bucket 11: 30%\n bucket 12: 40%\n bucket 11: 40%\n bucket 12: 50%\n bucket 11: 50%\n bucket 12: 60%\n bucket 11: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 29\n Entering block accumulator loop for bucket 13:\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 10%\n Entering block accumulator loop for bucket 14:\n bucket 13: 20%\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 14: 60%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\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": "2023-10-24 15:12:20", "plugin": "core", "name": "end_epoch", "raw_value": "1698160340.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:12:19", "plugin": "core", "name": "start_epoch", "raw_value": "1698160339.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-11", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 11, "time_seconds": 141.50657773017883, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "bb75fbafb952325c"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "d6bfcc6aa312465a"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "c67cb6056660516f", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:14:52.321736", "create_time": "2023-10-24T15:12:42.651450", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-csr58", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/8/9/f/dataset_89fbefc1-4e74-4ad4-8bc4-bb96fbf9f06c.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/6/a/f/dataset_6af451e6-a900-4679-9f5c-7e600d5a4cf2.dat' > input_f.fastq && seqtk seq -2 '/galaxy/server/database/objects/6/a/f/dataset_6af451e6-a900-4679-9f5c-7e600d5a4cf2.dat' > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/d/3/d/dataset_d3d968e6-60f4-4e49-aed5-3208f502e5d2.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 224, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 223, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "bb75fbafb952325c", "src": "hda", "uuid": "89fbefc1-4e74-4ad4-8bc4-bb96fbf9f06c"}, "input_1": {"id": "d6bfcc6aa312465a", "src": "hda", "uuid": "6af451e6-a900-4679-9f5c-7e600d5a4cf2"}}, "outputs": {"output_alignments": {"id": "fb1fd6ba9aa67c1c", "src": "hda", "uuid": "d3d968e6-60f4-4e49-aed5-3208f502e5d2"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\nGetting block 3 of 29\n Reserving size (252) for bucket 3\nGetting block 2 of 29\nGetting block 4 of 29\n Reserving size (252) for bucket 2\n Reserving size (252) for bucket 1\n Reserving size (252) for bucket 4\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 4:\n bucket 3: 10%\n bucket 1: 10%\n bucket 2: 10%\n bucket 1: 20%\n bucket 2: 20%\n bucket 3: 20%\n bucket 4: 10%\n bucket 1: 30%\n bucket 2: 30%\n bucket 4: 20%\n bucket 2: 40%\n bucket 1: 40%\n bucket 3: 30%\n bucket 4: 30%\n bucket 1: 50%\n bucket 3: 40%\n bucket 4: 40%\n bucket 2: 50%\n bucket 1: 60%\n bucket 4: 50%\n bucket 3: 50%\n bucket 2: 60%\n bucket 1: 70%\n bucket 4: 60%\n bucket 3: 60%\n bucket 1: 80%\n bucket 2: 70%\n bucket 1: 90%\n bucket 3: 70%\n bucket 4: 70%\n bucket 2: 80%\n bucket 4: 80%\n bucket 1: 100%\n bucket 3: 80%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 4: 90%\n bucket 3: 90%\n bucket 2: 90%\n bucket 4: 100%\n bucket 3: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block of length 166 for bucket 3\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\nGetting block 6 of 29\n Calculating Z arrays for bucket 5\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n Entering block accumulator loop for bucket 6:\n bucket 5: 10%\n bucket 6: 10%\n bucket 5: 20%\n bucket 6: 20%\n bucket 5: 30%\n bucket 6: 30%\n bucket 5: 40%\n bucket 6: 40%\n bucket 5: 50%\n bucket 6: 50%\n bucket 5: 60%\n bucket 6: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 6: 70%\n bucket 5: 90%\n bucket 6: 80%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\nGetting block 8 of 29\n bucket 7: 10%\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n bucket 7: 20%\n bucket 7: 30%\n Entering block accumulator loop for bucket 8:\n bucket 7: 40%\n bucket 7: 50%\n bucket 8: 10%\n bucket 7: 60%\n bucket 8: 20%\n bucket 7: 70%\n bucket 8: 30%\n bucket 7: 80%\n bucket 8: 40%\n bucket 7: 90%\n bucket 8: 50%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n bucket 9: 50%\n Calculating Z arrays for bucket 10\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n Entering block accumulator loop for bucket 10:\n bucket 9: 90%\n bucket 9: 100%\n bucket 10: 10%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 12:\n bucket 11: 10%\n bucket 12: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 12: 20%\n bucket 11: 40%\n bucket 12: 30%\n bucket 11: 50%\n bucket 12: 40%\n bucket 11: 60%\n bucket 12: 50%\n bucket 11: 70%\n bucket 12: 60%\n bucket 11: 80%\n bucket 12: 70%\n bucket 11: 90%\n bucket 12: 80%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\nGetting block 14 of 29\n bucket 13: 10%\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 20%\n Entering block accumulator loop for bucket 14:\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 14: 60%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n bucket 14: 80%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nReturning block of 198 for bucket 13\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\nGetting block 18 of 29\n bucket 17: 70%\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 80%\n bucket 17: 90%\n Entering block accumulator loop for bucket 18:\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\nGetting block 20 of 29\n bucket 19: 50%\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 60%\n bucket 19: 70%\n Entering block accumulator loop for bucket 20:\n bucket 19: 80%\n bucket 20: 10%\n bucket 19: 90%\n bucket 20: 20%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 162 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\nGetting block 24 of 29\n bucket 23: 40%\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 50%\n bucket 23: 60%\n Entering block accumulator loop for bucket 24:\n bucket 23: 70%\n bucket 23: 80%\n bucket 24: 10%\n bucket 23: 90%\n bucket 24: 20%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\nGetting block 27 of 29\n bucket 26: 60%\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n Entering block accumulator loop for bucket 27:\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\nGetting block 3 of 29\n Reserving size (252) for bucket 3\nGetting block 2 of 29\nGetting block 4 of 29\n Reserving size (252) for bucket 2\n Reserving size (252) for bucket 1\n Reserving size (252) for bucket 4\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 4:\n bucket 3: 10%\n bucket 1: 10%\n bucket 2: 10%\n bucket 1: 20%\n bucket 2: 20%\n bucket 3: 20%\n bucket 4: 10%\n bucket 1: 30%\n bucket 2: 30%\n bucket 4: 20%\n bucket 2: 40%\n bucket 1: 40%\n bucket 3: 30%\n bucket 4: 30%\n bucket 1: 50%\n bucket 3: 40%\n bucket 4: 40%\n bucket 2: 50%\n bucket 1: 60%\n bucket 4: 50%\n bucket 3: 50%\n bucket 2: 60%\n bucket 1: 70%\n bucket 4: 60%\n bucket 3: 60%\n bucket 1: 80%\n bucket 2: 70%\n bucket 1: 90%\n bucket 3: 70%\n bucket 4: 70%\n bucket 2: 80%\n bucket 4: 80%\n bucket 1: 100%\n bucket 3: 80%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 4: 90%\n bucket 3: 90%\n bucket 2: 90%\n bucket 4: 100%\n bucket 3: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block of length 166 for bucket 3\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\nGetting block 6 of 29\n Calculating Z arrays for bucket 5\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n Entering block accumulator loop for bucket 6:\n bucket 5: 10%\n bucket 6: 10%\n bucket 5: 20%\n bucket 6: 20%\n bucket 5: 30%\n bucket 6: 30%\n bucket 5: 40%\n bucket 6: 40%\n bucket 5: 50%\n bucket 6: 50%\n bucket 5: 60%\n bucket 6: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 6: 70%\n bucket 5: 90%\n bucket 6: 80%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\nGetting block 8 of 29\n bucket 7: 10%\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n bucket 7: 20%\n bucket 7: 30%\n Entering block accumulator loop for bucket 8:\n bucket 7: 40%\n bucket 7: 50%\n bucket 8: 10%\n bucket 7: 60%\n bucket 8: 20%\n bucket 7: 70%\n bucket 8: 30%\n bucket 7: 80%\n bucket 8: 40%\n bucket 7: 90%\n bucket 8: 50%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n bucket 9: 50%\n Calculating Z arrays for bucket 10\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n Entering block accumulator loop for bucket 10:\n bucket 9: 90%\n bucket 9: 100%\n bucket 10: 10%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 12:\n bucket 11: 10%\n bucket 12: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 12: 20%\n bucket 11: 40%\n bucket 12: 30%\n bucket 11: 50%\n bucket 12: 40%\n bucket 11: 60%\n bucket 12: 50%\n bucket 11: 70%\n bucket 12: 60%\n bucket 11: 80%\n bucket 12: 70%\n bucket 11: 90%\n bucket 12: 80%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\nGetting block 14 of 29\n bucket 13: 10%\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 20%\n Entering block accumulator loop for bucket 14:\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 14: 60%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n bucket 14: 80%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nReturning block of 198 for bucket 13\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\nGetting block 18 of 29\n bucket 17: 70%\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 80%\n bucket 17: 90%\n Entering block accumulator loop for bucket 18:\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\nGetting block 20 of 29\n bucket 19: 50%\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 60%\n bucket 19: 70%\n Entering block accumulator loop for bucket 20:\n bucket 19: 80%\n bucket 20: 10%\n bucket 19: 90%\n bucket 20: 20%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 162 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\nGetting block 24 of 29\n bucket 23: 40%\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 50%\n bucket 23: 60%\n Entering block accumulator loop for bucket 24:\n bucket 23: 70%\n bucket 23: 80%\n bucket 24: 10%\n bucket 23: 90%\n bucket 24: 20%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\nGetting block 27 of 29\n bucket 26: 60%\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n Entering block accumulator loop for bucket 27:\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "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": "2023-10-24 15:14:41", "plugin": "core", "name": "end_epoch", "raw_value": "1698160481.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:14:41", "plugin": "core", "name": "start_epoch", "raw_value": "1698160481.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-12", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 12, "time_seconds": 132.83212685585022, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "ef8cbdbdbee26f7f"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "ba67786ce208b36e"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "ab80dd031322ef0b", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:17:05.463215", "create_time": "2023-10-24T15:15:04.692372", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-7fj65", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/7/6/5/dataset_765af78a-225f-4d61-b192-f7cb65e5a90f.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && bzcat '/galaxy/server/database/objects/e/5/a/dataset_e5a6f479-802b-44d6-b8af-bf05802e43d7.dat' | seqtk seq -1 /dev/stdin > input_f.fastq && bzcat '/galaxy/server/database/objects/e/5/a/dataset_e5a6f479-802b-44d6-b8af-bf05802e43d7.dat' | seqtk seq -2 /dev/stdin > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/e/b/a/dataset_eba071fa-9245-4b8a-9c14-10c3b6f3fa71.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 227, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 226, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "ef8cbdbdbee26f7f", "src": "hda", "uuid": "765af78a-225f-4d61-b192-f7cb65e5a90f"}, "input_1": {"id": "ba67786ce208b36e", "src": "hda", "uuid": "e5a6f479-802b-44d6-b8af-bf05802e43d7"}}, "outputs": {"output_alignments": {"id": "aea06e5a7e1dce0a", "src": "hda", "uuid": "eba071fa-9245-4b8a-9c14-10c3b6f3fa71"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\nGetting block 2 of 29\n Reserving size (252) for bucket 1\n Reserving size (252) for bucket 2\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\n bucket 1: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 4:\n bucket 3: 10%\n bucket 1: 30%\n bucket 2: 10%\n bucket 4: 10%\n bucket 1: 40%\n bucket 3: 20%\n bucket 2: 20%\n bucket 1: 50%\n bucket 4: 20%\n bucket 3: 30%\n bucket 2: 30%\n bucket 1: 60%\n bucket 4: 30%\n bucket 3: 40%\n bucket 2: 40%\n bucket 1: 70%\n bucket 4: 40%\n bucket 3: 50%\n bucket 1: 80%\n bucket 2: 50%\n bucket 4: 50%\n bucket 1: 90%\n bucket 3: 60%\n bucket 2: 60%\n bucket 4: 60%\n bucket 1: 100%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 3: 70%\n bucket 4: 70%\n bucket 2: 70%\n bucket 3: 80%\n bucket 4: 80%\n bucket 2: 80%\n bucket 4: 90%\n bucket 3: 90%\n bucket 2: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n bucket 3: 100%\n bucket 2: 100%\n Sorting block of length 166 for bucket 3\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n bucket 5: 10%\n Calculating Z arrays for bucket 6\n bucket 5: 20%\n bucket 5: 30%\n Entering block accumulator loop for bucket 6:\n bucket 5: 40%\n bucket 6: 10%\n bucket 5: 50%\n bucket 6: 20%\n bucket 5: 60%\n bucket 6: 30%\n bucket 6: 40%\n bucket 5: 70%\n bucket 6: 50%\n bucket 5: 80%\n bucket 6: 60%\n bucket 5: 90%\n bucket 6: 70%\n bucket 5: 100%\n bucket 6: 80%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n Sorting block time: 00:00:00\n bucket 12: 20%\nReturning block of 230 for bucket 11\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n bucket 13: 20%\n Calculating Z arrays for bucket 14\n bucket 13: 30%\n Entering block accumulator loop for bucket 14:\n bucket 13: 40%\n bucket 14: 10%\n bucket 13: 50%\n bucket 14: 20%\n bucket 13: 60%\n bucket 14: 30%\n bucket 13: 70%\n bucket 14: 40%\n bucket 13: 80%\n bucket 14: 50%\n bucket 13: 90%\n bucket 14: 60%\n bucket 13: 100%\n bucket 14: 70%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n bucket 23: 90%\n Calculating Z arrays for bucket 24\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 29\n Entering block accumulator loop for bucket 27:\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 10%\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 28: 10%\n bucket 27: 30%\n bucket 28: 20%\n bucket 27: 40%\n bucket 28: 30%\n bucket 27: 50%\n bucket 28: 40%\n bucket 28: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 28: 60%\n bucket 27: 80%\n bucket 28: 70%\n bucket 27: 90%\n bucket 27: 100%\n bucket 28: 80%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\nGetting block 2 of 29\n Reserving size (252) for bucket 1\n Reserving size (252) for bucket 2\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\n bucket 1: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 4:\n bucket 3: 10%\n bucket 1: 30%\n bucket 2: 10%\n bucket 4: 10%\n bucket 1: 40%\n bucket 3: 20%\n bucket 2: 20%\n bucket 1: 50%\n bucket 4: 20%\n bucket 3: 30%\n bucket 2: 30%\n bucket 1: 60%\n bucket 4: 30%\n bucket 3: 40%\n bucket 2: 40%\n bucket 1: 70%\n bucket 4: 40%\n bucket 3: 50%\n bucket 1: 80%\n bucket 2: 50%\n bucket 4: 50%\n bucket 1: 90%\n bucket 3: 60%\n bucket 2: 60%\n bucket 4: 60%\n bucket 1: 100%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 3: 70%\n bucket 4: 70%\n bucket 2: 70%\n bucket 3: 80%\n bucket 4: 80%\n bucket 2: 80%\n bucket 4: 90%\n bucket 3: 90%\n bucket 2: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n bucket 3: 100%\n bucket 2: 100%\n Sorting block of length 166 for bucket 3\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n bucket 5: 10%\n Calculating Z arrays for bucket 6\n bucket 5: 20%\n bucket 5: 30%\n Entering block accumulator loop for bucket 6:\n bucket 5: 40%\n bucket 6: 10%\n bucket 5: 50%\n bucket 6: 20%\n bucket 5: 60%\n bucket 6: 30%\n bucket 6: 40%\n bucket 5: 70%\n bucket 6: 50%\n bucket 5: 80%\n bucket 6: 60%\n bucket 5: 90%\n bucket 6: 70%\n bucket 5: 100%\n bucket 6: 80%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n Sorting block time: 00:00:00\n bucket 12: 20%\nReturning block of 230 for bucket 11\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n bucket 13: 20%\n Calculating Z arrays for bucket 14\n bucket 13: 30%\n Entering block accumulator loop for bucket 14:\n bucket 13: 40%\n bucket 14: 10%\n bucket 13: 50%\n bucket 14: 20%\n bucket 13: 60%\n bucket 14: 30%\n bucket 13: 70%\n bucket 14: 40%\n bucket 13: 80%\n bucket 14: 50%\n bucket 13: 90%\n bucket 14: 60%\n bucket 13: 100%\n bucket 14: 70%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n bucket 23: 90%\n Calculating Z arrays for bucket 24\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 29\n Entering block accumulator loop for bucket 27:\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 10%\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 28: 10%\n bucket 27: 30%\n bucket 28: 20%\n bucket 27: 40%\n bucket 28: 30%\n bucket 27: 50%\n bucket 28: 40%\n bucket 28: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 28: 60%\n bucket 27: 80%\n bucket 28: 70%\n bucket 27: 90%\n bucket 27: 100%\n bucket 28: 80%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\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": "2023-10-24 15:16:55", "plugin": "core", "name": "end_epoch", "raw_value": "1698160615.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:16:54", "plugin": "core", "name": "start_epoch", "raw_value": "1698160614.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-13", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 13, "time_seconds": 138.50521731376648, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "eac31ad5382689a5"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "3284790508cce86f"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "a8c9e8d3ad346a3f", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:19:23.974946", "create_time": "2023-10-24T15:17:17.149157", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-9xwq9", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/b/a/5/dataset_ba5852ab-a0f0-4f65-b642-7188bd9c9150.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/2/d/0/dataset_2d0ac1f8-38e2-4196-a2c5-8a8235f7e74b.dat' > input_f.fastq && seqtk seq -2 '/galaxy/server/database/objects/2/d/0/dataset_2d0ac1f8-38e2-4196-a2c5-8a8235f7e74b.dat' > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/4/a/1/dataset_4a16caa4-2d82-4118-ba2e-c3e2034286d4.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 230, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 229, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "eac31ad5382689a5", "src": "hda", "uuid": "ba5852ab-a0f0-4f65-b642-7188bd9c9150"}, "input_1": {"id": "3284790508cce86f", "src": "hda", "uuid": "2d0ac1f8-38e2-4196-a2c5-8a8235f7e74b"}}, "outputs": {"output_alignments": {"id": "7342fa5dce26c277", "src": "hda", "uuid": "4a16caa4-2d82-4118-ba2e-c3e2034286d4"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\n Entering block accumulator loop for bucket 1:\n Reserving size (252) for bucket 2\nGetting block 3 of 29\n Calculating Z arrays for bucket 2\n Reserving size (252) for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n bucket 1: 20%\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n Entering block accumulator loop for bucket 3:\n bucket 2: 10%\n bucket 1: 40%\n bucket 2: 20%\n bucket 3: 10%\n bucket 1: 50%\n bucket 2: 30%\nGetting block 4 of 29\n bucket 3: 20%\n bucket 2: 40%\n Reserving size (252) for bucket 4\n bucket 1: 60%\n bucket 2: 50%\n Calculating Z arrays for bucket 4\n bucket 3: 30%\n bucket 1: 70%\n bucket 2: 60%\n bucket 3: 40%\n bucket 1: 80%\n bucket 2: 70%\n bucket 3: 50%\n bucket 1: 90%\n Entering block accumulator loop for bucket 4:\n bucket 2: 80%\n bucket 1: 100%\n bucket 3: 60%\n Sorting block of length 127 for bucket 1\n bucket 2: 90%\n bucket 4: 10%\n bucket 3: 70%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n bucket 3: 80%\n bucket 4: 20%\n bucket 3: 90%\n (Using difference cover)\n bucket 4: 30%\n bucket 3: 100%\n bucket 4: 40%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 4: 50%\n bucket 4: 60%\n bucket 4: 70%\n bucket 4: 80%\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 6:\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\nGetting block 8 of 29\n bucket 7: 70%\n Reserving size (252) for bucket 8\n bucket 7: 80%\n Calculating Z arrays for bucket 8\n bucket 7: 90%\n Entering block accumulator loop for bucket 8:\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n Sorting block time: 00:00:00\n bucket 8: 80%\nReturning block of 221 for bucket 7\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\nGetting block 17 of 29\n Calculating Z arrays for bucket 16\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n Entering block accumulator loop for bucket 16:\n bucket 17: 20%\n bucket 17: 30%\n bucket 16: 10%\n bucket 17: 40%\n bucket 16: 20%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 16: 30%\n bucket 17: 80%\n bucket 16: 40%\n bucket 17: 90%\n bucket 16: 50%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n bucket 18: 70%\n Calculating Z arrays for bucket 19\n bucket 18: 80%\n bucket 18: 90%\n Entering block accumulator loop for bucket 19:\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 29\n Entering block accumulator loop for bucket 22:\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 10%\n bucket 22: 20%\n Entering block accumulator loop for bucket 23:\n bucket 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n bucket 23: 20%\n bucket 22: 50%\n bucket 23: 30%\n bucket 22: 60%\n bucket 23: 40%\n bucket 22: 70%\n bucket 23: 50%\n bucket 22: 80%\n bucket 23: 60%\n bucket 22: 90%\n bucket 23: 70%\n bucket 22: 100%\n bucket 23: 80%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 20%\n bucket 24: 30%\n Entering block accumulator loop for bucket 25:\n bucket 24: 40%\n bucket 25: 10%\n bucket 24: 50%\n bucket 25: 20%\n bucket 24: 60%\n bucket 25: 30%\n bucket 24: 70%\n bucket 25: 40%\n bucket 24: 80%\n bucket 25: 50%\n bucket 24: 90%\n bucket 25: 60%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\n Entering block accumulator loop for bucket 1:\n Reserving size (252) for bucket 2\nGetting block 3 of 29\n Calculating Z arrays for bucket 2\n Reserving size (252) for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n bucket 1: 20%\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n Entering block accumulator loop for bucket 3:\n bucket 2: 10%\n bucket 1: 40%\n bucket 2: 20%\n bucket 3: 10%\n bucket 1: 50%\n bucket 2: 30%\nGetting block 4 of 29\n bucket 3: 20%\n bucket 2: 40%\n Reserving size (252) for bucket 4\n bucket 1: 60%\n bucket 2: 50%\n Calculating Z arrays for bucket 4\n bucket 3: 30%\n bucket 1: 70%\n bucket 2: 60%\n bucket 3: 40%\n bucket 1: 80%\n bucket 2: 70%\n bucket 3: 50%\n bucket 1: 90%\n Entering block accumulator loop for bucket 4:\n bucket 2: 80%\n bucket 1: 100%\n bucket 3: 60%\n Sorting block of length 127 for bucket 1\n bucket 2: 90%\n bucket 4: 10%\n bucket 3: 70%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n bucket 3: 80%\n bucket 4: 20%\n bucket 3: 90%\n (Using difference cover)\n bucket 4: 30%\n bucket 3: 100%\n bucket 4: 40%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 4: 50%\n bucket 4: 60%\n bucket 4: 70%\n bucket 4: 80%\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 6:\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\nGetting block 8 of 29\n bucket 7: 70%\n Reserving size (252) for bucket 8\n bucket 7: 80%\n Calculating Z arrays for bucket 8\n bucket 7: 90%\n Entering block accumulator loop for bucket 8:\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n Sorting block time: 00:00:00\n bucket 8: 80%\nReturning block of 221 for bucket 7\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\nGetting block 17 of 29\n Calculating Z arrays for bucket 16\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n Entering block accumulator loop for bucket 16:\n bucket 17: 20%\n bucket 17: 30%\n bucket 16: 10%\n bucket 17: 40%\n bucket 16: 20%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 16: 30%\n bucket 17: 80%\n bucket 16: 40%\n bucket 17: 90%\n bucket 16: 50%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n bucket 18: 70%\n Calculating Z arrays for bucket 19\n bucket 18: 80%\n bucket 18: 90%\n Entering block accumulator loop for bucket 19:\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 29\n Entering block accumulator loop for bucket 22:\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 10%\n bucket 22: 20%\n Entering block accumulator loop for bucket 23:\n bucket 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n bucket 23: 20%\n bucket 22: 50%\n bucket 23: 30%\n bucket 22: 60%\n bucket 23: 40%\n bucket 22: 70%\n bucket 23: 50%\n bucket 22: 80%\n bucket 23: 60%\n bucket 22: 90%\n bucket 23: 70%\n bucket 22: 100%\n bucket 23: 80%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 20%\n bucket 24: 30%\n Entering block accumulator loop for bucket 25:\n bucket 24: 40%\n bucket 25: 10%\n bucket 24: 50%\n bucket 25: 20%\n bucket 24: 60%\n bucket 25: 30%\n bucket 24: 70%\n bucket 25: 40%\n bucket 24: 80%\n bucket 25: 50%\n bucket 24: 90%\n bucket 25: 60%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "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": "2023-10-24 15:19:13", "plugin": "core", "name": "end_epoch", "raw_value": "1698160753.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:19:13", "plugin": "core", "name": "start_epoch", "raw_value": "1698160753.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-14", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 14, "time_seconds": 131.9051992893219, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "ffd10c3bb044c57d"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "36b5feefaed59460"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "60653eca26084f85", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:21:36.035502", "create_time": "2023-10-24T15:19:35.802999", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-g7x7q", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/7/f/f/dataset_7ff3b3a6-3fd3-4d81-81df-dbbd444c917d.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/f/0/b/dataset_f0b5e168-729f-4e8b-ab4b-18d0439ddd4d.dat' > input_f.fasta && seqtk seq -2 '/galaxy/server/database/objects/f/0/b/dataset_f0b5e168-729f-4e8b-ab4b-18d0439ddd4d.dat' > input_r.fasta && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -f -1 input_f.fasta -2 input_r.fasta | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/d/0/b/dataset_d0b35462-b2f4-4e7a-9f86-2cf5172df674.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 233, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 232, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "ffd10c3bb044c57d", "src": "hda", "uuid": "7ff3b3a6-3fd3-4d81-81df-dbbd444c917d"}, "input_1": {"id": "36b5feefaed59460", "src": "hda", "uuid": "f0b5e168-729f-4e8b-ab4b-18d0439ddd4d"}}, "outputs": {"output_alignments": {"id": "3fef656fe2fdcdc7", "src": "hda", "uuid": "d0b35462-b2f4-4e7a-9f86-2cf5172df674"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\n Entering block accumulator loop for bucket 1:\n Reserving size (252) for bucket 2\n Calculating Z arrays for bucket 2\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 3\nGetting block 4 of 29\n Entering block accumulator loop for bucket 3:\n bucket 2: 10%\n Reserving size (252) for bucket 4\n bucket 1: 10%\n bucket 2: 20%\n Calculating Z arrays for bucket 4\n bucket 3: 10%\n bucket 2: 30%\n bucket 1: 20%\n bucket 3: 20%\n bucket 2: 40%\n bucket 1: 30%\n bucket 3: 30%\n bucket 2: 50%\n Entering block accumulator loop for bucket 4:\n bucket 1: 40%\n bucket 3: 40%\n bucket 2: 60%\n bucket 1: 50%\n bucket 4: 10%\n bucket 2: 70%\n bucket 3: 50%\n bucket 1: 60%\n bucket 4: 20%\n bucket 2: 80%\n bucket 3: 60%\n bucket 1: 70%\n bucket 4: 30%\n bucket 2: 90%\n bucket 1: 80%\n bucket 3: 70%\n bucket 4: 40%\n bucket 1: 90%\n bucket 3: 80%\n bucket 2: 100%\n bucket 4: 50%\n bucket 1: 100%\n bucket 3: 90%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n Sorting block of length 239 for bucket 2\n bucket 4: 60%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 4: 70%\n bucket 4: 80%\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 6:\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n bucket 13: 100%\n Calculating Z arrays for bucket 14\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n Sorting block time: 00:00:00\n bucket 14: 80%\nReturning block of 198 for bucket 13\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 16: 10%\n bucket 15: 20%\n bucket 16: 20%\n bucket 15: 30%\n bucket 16: 30%\n bucket 15: 40%\n bucket 16: 40%\n bucket 15: 50%\n bucket 16: 50%\n bucket 15: 60%\n bucket 16: 60%\n bucket 15: 70%\n bucket 16: 70%\n bucket 15: 80%\n bucket 16: 80%\n bucket 15: 90%\n bucket 16: 90%\n bucket 15: 100%\n bucket 16: 100%\n Sorting block of length 177 for bucket 15\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 29\n Entering block accumulator loop for bucket 17:\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 10%\n bucket 17: 20%\n Entering block accumulator loop for bucket 18:\n bucket 17: 30%\n bucket 18: 10%\n bucket 17: 40%\n bucket 18: 20%\n bucket 17: 50%\n bucket 17: 60%\n bucket 18: 30%\n bucket 17: 70%\n bucket 18: 40%\n bucket 17: 80%\n bucket 18: 50%\n bucket 17: 90%\n bucket 18: 60%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\nGetting block 22 of 29\n Reserving size (252) for bucket 21\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 21\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 21: 10%\n bucket 22: 20%\n bucket 21: 20%\n bucket 22: 30%\n bucket 21: 30%\n bucket 22: 40%\n bucket 21: 40%\n bucket 22: 50%\n bucket 21: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 21: 60%\n bucket 22: 80%\n bucket 21: 70%\n bucket 22: 90%\n bucket 22: 100%\n bucket 21: 80%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 25: 50%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 25: 60%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 28: 10%\n bucket 27: 30%\n bucket 28: 20%\n bucket 27: 40%\n bucket 28: 30%\n bucket 27: 50%\n bucket 28: 40%\n bucket 27: 60%\n bucket 28: 50%\n bucket 27: 70%\n bucket 28: 60%\n bucket 27: 80%\n bucket 28: 70%\n bucket 27: 90%\n bucket 28: 80%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 3 (30.00%) aligned concordantly 0 times\n 7 (70.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 3 (50.00%) aligned 0 times\n 3 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n85.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 3 (30.00%) aligned concordantly 0 times\n 7 (70.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 3 (50.00%) aligned 0 times\n 3 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n85.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\n Entering block accumulator loop for bucket 1:\n Reserving size (252) for bucket 2\n Calculating Z arrays for bucket 2\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 3\nGetting block 4 of 29\n Entering block accumulator loop for bucket 3:\n bucket 2: 10%\n Reserving size (252) for bucket 4\n bucket 1: 10%\n bucket 2: 20%\n Calculating Z arrays for bucket 4\n bucket 3: 10%\n bucket 2: 30%\n bucket 1: 20%\n bucket 3: 20%\n bucket 2: 40%\n bucket 1: 30%\n bucket 3: 30%\n bucket 2: 50%\n Entering block accumulator loop for bucket 4:\n bucket 1: 40%\n bucket 3: 40%\n bucket 2: 60%\n bucket 1: 50%\n bucket 4: 10%\n bucket 2: 70%\n bucket 3: 50%\n bucket 1: 60%\n bucket 4: 20%\n bucket 2: 80%\n bucket 3: 60%\n bucket 1: 70%\n bucket 4: 30%\n bucket 2: 90%\n bucket 1: 80%\n bucket 3: 70%\n bucket 4: 40%\n bucket 1: 90%\n bucket 3: 80%\n bucket 2: 100%\n bucket 4: 50%\n bucket 1: 100%\n bucket 3: 90%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n Sorting block of length 239 for bucket 2\n bucket 4: 60%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 4: 70%\n bucket 4: 80%\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 6:\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n bucket 13: 100%\n Calculating Z arrays for bucket 14\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n Sorting block time: 00:00:00\n bucket 14: 80%\nReturning block of 198 for bucket 13\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 16: 10%\n bucket 15: 20%\n bucket 16: 20%\n bucket 15: 30%\n bucket 16: 30%\n bucket 15: 40%\n bucket 16: 40%\n bucket 15: 50%\n bucket 16: 50%\n bucket 15: 60%\n bucket 16: 60%\n bucket 15: 70%\n bucket 16: 70%\n bucket 15: 80%\n bucket 16: 80%\n bucket 15: 90%\n bucket 16: 90%\n bucket 15: 100%\n bucket 16: 100%\n Sorting block of length 177 for bucket 15\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 29\n Entering block accumulator loop for bucket 17:\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 10%\n bucket 17: 20%\n Entering block accumulator loop for bucket 18:\n bucket 17: 30%\n bucket 18: 10%\n bucket 17: 40%\n bucket 18: 20%\n bucket 17: 50%\n bucket 17: 60%\n bucket 18: 30%\n bucket 17: 70%\n bucket 18: 40%\n bucket 17: 80%\n bucket 18: 50%\n bucket 17: 90%\n bucket 18: 60%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\nGetting block 22 of 29\n Reserving size (252) for bucket 21\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 21\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 21: 10%\n bucket 22: 20%\n bucket 21: 20%\n bucket 22: 30%\n bucket 21: 30%\n bucket 22: 40%\n bucket 21: 40%\n bucket 22: 50%\n bucket 21: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 21: 60%\n bucket 22: 80%\n bucket 21: 70%\n bucket 22: 90%\n bucket 22: 100%\n bucket 21: 80%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 25: 50%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 25: 60%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 28: 10%\n bucket 27: 30%\n bucket 28: 20%\n bucket 27: 40%\n bucket 28: 30%\n bucket 27: 50%\n bucket 28: 40%\n bucket 27: 60%\n bucket 28: 50%\n bucket 27: 70%\n bucket 28: 60%\n bucket 27: 80%\n bucket 28: 70%\n bucket 27: 90%\n bucket 28: 80%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\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": "2023-10-24 15:21:26", "plugin": "core", "name": "end_epoch", "raw_value": "1698160886.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:21:25", "plugin": "core", "name": "start_epoch", "raw_value": "1698160885.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-15", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 15, "time_seconds": 137.68643999099731, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "493448ca597c0312"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "5a923d6c951850eb"}, "library|rna_strandness": "R", "library|type": "single", "adv|spliced_options|novel_splicesite_outfile": true, "adv|spliced_options|spliced_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "cbf74323d67c1126", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:23:52.889197", "create_time": "2023-10-24T15:21:47.417221", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-cf5pd", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/e/f/e/dataset_efe2fed8-6ba0-44eb-893d-ffca93bb0904.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/a/e/4/dataset_ae4c34fa-8a23-44f3-916d-c51691f2a6eb.dat' input_f.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -U 'input_f.fastq' --rna-strandness R --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000 --novel-splicesite-outfile '/galaxy/server/database/objects/1/7/d/dataset_17d1a060-4612-48cb-bd8f-96a71999bc13.dat' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/2/2/0/dataset_2203e4ab-37e1-49d4-8a73-a7f007263692.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 1, \"canonical_penalty\": \"0\", \"coefficient\": \"1.0\", \"constant_term\": \"-8.0\", \"function_type\": \"G\", \"known_splice_gtf\": null, \"max_intron\": \"500000\", \"min_intron\": \"20\", \"nc_coefficient\": \"1.0\", \"nc_constant_term\": \"-8.0\", \"nc_function_type\": \"G\", \"no_spliced_alignment_options\": {\"__current_case__\": 1, \"no_spliced_alignment\": \"\"}, \"noncanonical_penalty\": \"12\", \"notmplen\": \"false\", \"novel_splicesite_outfile\": \"true\", \"spliced_options_selector\": \"advanced\", \"tma\": \"\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 236, \"src\": \"hda\"}]}, \"rna_strandness\": \"R\", \"type\": \"single\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 235, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "493448ca597c0312", "src": "hda", "uuid": "efe2fed8-6ba0-44eb-893d-ffca93bb0904"}, "input_1": {"id": "5a923d6c951850eb", "src": "hda", "uuid": "ae4c34fa-8a23-44f3-916d-c51691f2a6eb"}}, "outputs": {"output_alignments": {"id": "0cd680c1664294fd", "src": "hda", "uuid": "2203e4ab-37e1-49d4-8a73-a7f007263692"}, "novel_splicesite_output": {"id": "27f51a418db17cab", "src": "hda", "uuid": "17d1a060-4612-48cb-bd8f-96a71999bc13"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\n bucket 1: 20%\nGetting block 2 of 29\n Reserving size (252) for bucket 2\nGetting block 3 of 29\n bucket 1: 30%\nGetting block 4 of 29\n Reserving size (252) for bucket 3\n bucket 1: 40%\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 2\n Reserving size (252) for bucket 4\n bucket 1: 50%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 2:\n bucket 1: 60%\n bucket 3: 10%\n Entering block accumulator loop for bucket 4:\n bucket 1: 70%\n bucket 3: 20%\n bucket 2: 10%\n bucket 1: 80%\n bucket 4: 10%\n bucket 1: 90%\n bucket 3: 30%\n bucket 4: 20%\n bucket 3: 40%\n bucket 1: 100%\n bucket 4: 30%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 3: 50%\n bucket 4: 40%\n bucket 3: 60%\n bucket 4: 50%\n bucket 3: 70%\n bucket 4: 60%\n bucket 3: 80%\n bucket 4: 70%\n bucket 3: 90%\n bucket 4: 80%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n bucket 4: 90%\n bucket 2: 20%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n bucket 2: 30%\n bucket 2: 40%\n bucket 2: 50%\n (Using difference cover)\n bucket 2: 60%\n bucket 2: 70%\n bucket 2: 80%\n bucket 2: 90%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n bucket 5: 30%\n Calculating Z arrays for bucket 6\n bucket 5: 40%\n bucket 5: 50%\n Entering block accumulator loop for bucket 6:\n bucket 5: 60%\n bucket 6: 10%\n bucket 5: 70%\n bucket 6: 20%\n bucket 5: 80%\n bucket 6: 30%\n bucket 5: 90%\n bucket 6: 40%\n bucket 5: 100%\n bucket 6: 50%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 7:\n Entering block accumulator loop for bucket 8:\n bucket 7: 10%\n bucket 8: 10%\n bucket 7: 20%\n bucket 8: 20%\n bucket 7: 30%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 7: 40%\n bucket 8: 80%\n bucket 7: 50%\n bucket 8: 90%\n bucket 7: 60%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\nGetting block 10 of 29\n bucket 9: 60%\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 70%\n Entering block accumulator loop for bucket 10:\n bucket 9: 80%\n bucket 10: 10%\n bucket 9: 90%\n bucket 10: 20%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\nGetting block 12 of 29\n bucket 11: 50%\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 60%\n Entering block accumulator loop for bucket 12:\n bucket 11: 70%\n bucket 11: 80%\n bucket 12: 10%\n bucket 11: 90%\n bucket 12: 20%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\nGetting block 14 of 29\n bucket 13: 50%\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 60%\n bucket 13: 70%\n Entering block accumulator loop for bucket 14:\n bucket 13: 80%\n bucket 14: 10%\n bucket 13: 90%\n bucket 14: 20%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Entering block accumulator loop for bucket 16:\n Calculating Z arrays for bucket 17\n bucket 16: 10%\n Entering block accumulator loop for bucket 17:\n bucket 16: 20%\n bucket 16: 30%\n bucket 17: 10%\n bucket 16: 40%\n bucket 17: 20%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 29\n Entering block accumulator loop for bucket 24:\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 10%\n bucket 24: 20%\n Entering block accumulator loop for bucket 25:\n bucket 24: 30%\n bucket 25: 10%\n bucket 24: 40%\n bucket 25: 20%\n bucket 24: 50%\n bucket 25: 30%\n bucket 24: 60%\n bucket 25: 40%\n bucket 24: 70%\n bucket 25: 50%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were unpaired; of these:\n 0 (0.00%) aligned 0 times\n 10 (100.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n100.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were unpaired; of these:\n 0 (0.00%) aligned 0 times\n 10 (100.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n100.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\n bucket 1: 20%\nGetting block 2 of 29\n Reserving size (252) for bucket 2\nGetting block 3 of 29\n bucket 1: 30%\nGetting block 4 of 29\n Reserving size (252) for bucket 3\n bucket 1: 40%\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 2\n Reserving size (252) for bucket 4\n bucket 1: 50%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 2:\n bucket 1: 60%\n bucket 3: 10%\n Entering block accumulator loop for bucket 4:\n bucket 1: 70%\n bucket 3: 20%\n bucket 2: 10%\n bucket 1: 80%\n bucket 4: 10%\n bucket 1: 90%\n bucket 3: 30%\n bucket 4: 20%\n bucket 3: 40%\n bucket 1: 100%\n bucket 4: 30%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 3: 50%\n bucket 4: 40%\n bucket 3: 60%\n bucket 4: 50%\n bucket 3: 70%\n bucket 4: 60%\n bucket 3: 80%\n bucket 4: 70%\n bucket 3: 90%\n bucket 4: 80%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n bucket 4: 90%\n bucket 2: 20%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n bucket 2: 30%\n bucket 2: 40%\n bucket 2: 50%\n (Using difference cover)\n bucket 2: 60%\n bucket 2: 70%\n bucket 2: 80%\n bucket 2: 90%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n bucket 5: 30%\n Calculating Z arrays for bucket 6\n bucket 5: 40%\n bucket 5: 50%\n Entering block accumulator loop for bucket 6:\n bucket 5: 60%\n bucket 6: 10%\n bucket 5: 70%\n bucket 6: 20%\n bucket 5: 80%\n bucket 6: 30%\n bucket 5: 90%\n bucket 6: 40%\n bucket 5: 100%\n bucket 6: 50%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 7:\n Entering block accumulator loop for bucket 8:\n bucket 7: 10%\n bucket 8: 10%\n bucket 7: 20%\n bucket 8: 20%\n bucket 7: 30%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 7: 40%\n bucket 8: 80%\n bucket 7: 50%\n bucket 8: 90%\n bucket 7: 60%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\nGetting block 10 of 29\n bucket 9: 60%\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 70%\n Entering block accumulator loop for bucket 10:\n bucket 9: 80%\n bucket 10: 10%\n bucket 9: 90%\n bucket 10: 20%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\nGetting block 12 of 29\n bucket 11: 50%\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 60%\n Entering block accumulator loop for bucket 12:\n bucket 11: 70%\n bucket 11: 80%\n bucket 12: 10%\n bucket 11: 90%\n bucket 12: 20%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\nGetting block 14 of 29\n bucket 13: 50%\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 60%\n bucket 13: 70%\n Entering block accumulator loop for bucket 14:\n bucket 13: 80%\n bucket 14: 10%\n bucket 13: 90%\n bucket 14: 20%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Entering block accumulator loop for bucket 16:\n Calculating Z arrays for bucket 17\n bucket 16: 10%\n Entering block accumulator loop for bucket 17:\n bucket 16: 20%\n bucket 16: 30%\n bucket 17: 10%\n bucket 16: 40%\n bucket 17: 20%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 29\n Entering block accumulator loop for bucket 24:\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 10%\n bucket 24: 20%\n Entering block accumulator loop for bucket 25:\n bucket 24: 30%\n bucket 25: 10%\n bucket 24: 40%\n bucket 25: 20%\n bucket 24: 50%\n bucket 25: 30%\n bucket 24: 60%\n bucket 25: 40%\n bucket 24: 70%\n bucket 25: 50%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "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": "2023-10-24 15:23:42", "plugin": "core", "name": "end_epoch", "raw_value": "1698161022.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:23:42", "plugin": "core", "name": "start_epoch", "raw_value": "1698161022.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-16", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 16, "time_seconds": 134.07302594184875, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "3e8253d7eef34e29"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "27d5b8bbb1dbe4c8"}, "library|type": "paired_interleaved", "adv|sam_options|no_unal": true, "adv|sam_options|read_groups|read_groups_0|rg": "BC:test1", "adv|sam_options|read_groups|read_groups_1|rg": "CN:test2", "adv|sam_options|read_groups|rg_labels": "Yes", "adv|sam_options|chr_text": "--add-chrname", "adv|sam_options|omit_sec_seq": true, "adv|sam_options|sam_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "a536e486e3bf0b12", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:26:07.773973", "create_time": "2023-10-24T15:24:06.358998", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-4j72x", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/1/7/2/dataset_172441fb-ffa4-41ed-befa-3aee67df4254.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && bzcat '/galaxy/server/database/objects/3/b/c/dataset_3bc7353a-92ed-4673-9861-8bc87edd3c86.dat' | seqtk seq -1 /dev/stdin > input_f.fastq && bzcat '/galaxy/server/database/objects/3/b/c/dataset_3bc7353a-92ed-4673-9861-8bc87edd3c86.dat' | seqtk seq -2 /dev/stdin > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq --no-unal --rg-id 'read_group' --rg 'BC:test1' --rg 'CN:test2' --add-chrname --omit-sec-seq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/4/c/b/dataset_4cb80cd0-91c9-449c-9777-b8582cd0fb4a.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 1, \"chr_text\": \"--add-chrname\", \"no_unal\": \"true\", \"omit_sec_seq\": \"true\", \"read_groups\": {\"__current_case__\": 1, \"read_groups\": [{\"__index__\": 0, \"rg\": \"BC:test1\"}, {\"__index__\": 1, \"rg\": \"CN:test2\"}], \"rg_id\": \"read_group\", \"rg_labels\": \"Yes\"}, \"sam_options_selector\": \"advanced\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 240, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 239, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "3e8253d7eef34e29", "src": "hda", "uuid": "172441fb-ffa4-41ed-befa-3aee67df4254"}, "input_1": {"id": "27d5b8bbb1dbe4c8", "src": "hda", "uuid": "3bc7353a-92ed-4673-9861-8bc87edd3c86"}}, "outputs": {"output_alignments": {"id": "5fc64e921966f9fd", "src": "hda", "uuid": "4cb80cd0-91c9-449c-9777-b8582cd0fb4a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\nGetting block 3 of 29\n Entering block accumulator loop for bucket 1:\n Reserving size (252) for bucket 3\n Reserving size (252) for bucket 2\nGetting block 4 of 29\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 2\n bucket 1: 10%\n Reserving size (252) for bucket 4\n bucket 1: 20%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 2:\n bucket 3: 10%\n bucket 1: 30%\n bucket 3: 20%\n bucket 2: 10%\n bucket 3: 30%\n bucket 1: 40%\n Entering block accumulator loop for bucket 4:\n bucket 2: 20%\n bucket 1: 50%\n bucket 3: 40%\n bucket 4: 10%\n bucket 1: 60%\n bucket 3: 50%\n bucket 2: 30%\n bucket 1: 70%\n bucket 4: 20%\n bucket 3: 60%\n bucket 1: 80%\n bucket 2: 40%\n bucket 4: 30%\n bucket 3: 70%\n bucket 1: 90%\n bucket 2: 50%\n bucket 4: 40%\n bucket 3: 80%\n bucket 2: 60%\n bucket 1: 100%\n bucket 4: 50%\n Sorting block of length 127 for bucket 1\n bucket 3: 90%\n bucket 2: 70%\n (Using difference cover)\n bucket 4: 60%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 2: 80%\n bucket 4: 70%\n bucket 2: 90%\n bucket 4: 80%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n bucket 4: 90%\n (Using difference cover)\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 6:\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\nGetting block 8 of 29\n bucket 7: 10%\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n bucket 7: 20%\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 7: 30%\n bucket 8: 20%\n bucket 7: 40%\n bucket 7: 50%\n bucket 8: 30%\n bucket 7: 60%\n bucket 8: 40%\n bucket 7: 70%\n bucket 8: 50%\n bucket 7: 80%\n bucket 8: 60%\n bucket 7: 90%\n bucket 8: 70%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 9\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 9: 50%\n bucket 10: 50%\n bucket 9: 60%\n bucket 10: 60%\n bucket 10: 70%\n bucket 9: 70%\n bucket 10: 80%\n bucket 9: 80%\n bucket 10: 90%\n bucket 9: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 11 of 29\n Reserving size (252) for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 11:\n bucket 12: 10%\n bucket 11: 10%\n bucket 12: 20%\n bucket 11: 20%\n bucket 12: 30%\n bucket 11: 30%\n bucket 12: 40%\n bucket 11: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 11: 50%\n bucket 12: 70%\n bucket 11: 60%\n bucket 12: 80%\n bucket 11: 70%\n bucket 12: 90%\n bucket 11: 80%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 13 of 29\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 14\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 13:\n bucket 14: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 13: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 13: 30%\n bucket 14: 50%\n bucket 13: 40%\n bucket 14: 60%\n bucket 13: 50%\n bucket 14: 70%\n bucket 13: 60%\n bucket 14: 80%\n bucket 14: 90%\n bucket 13: 70%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n bucket 13: 80%\n (Using difference cover)\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Entering block accumulator loop for bucket 15:\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 16: 20%\n bucket 15: 40%\n bucket 16: 30%\n bucket 15: 50%\n bucket 16: 40%\n bucket 15: 60%\n bucket 16: 50%\n bucket 15: 70%\n bucket 16: 60%\n bucket 15: 80%\n bucket 16: 70%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n bucket 16: 80%\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n Entering block accumulator loop for bucket 20:\n bucket 19: 10%\n bucket 20: 10%\n bucket 19: 20%\n bucket 20: 20%\n bucket 19: 30%\n bucket 20: 30%\n bucket 19: 40%\n bucket 20: 40%\n bucket 19: 50%\n bucket 20: 50%\n bucket 19: 60%\n bucket 20: 60%\n bucket 19: 70%\n bucket 20: 70%\n bucket 19: 80%\n bucket 20: 80%\n bucket 19: 90%\n bucket 20: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\nGetting block 26 of 29\n Calculating Z arrays for bucket 25\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 26:\n bucket 25: 10%\n bucket 26: 10%\n bucket 25: 20%\n bucket 26: 20%\n bucket 25: 30%\n bucket 26: 30%\n bucket 25: 40%\n bucket 26: 40%\n bucket 25: 50%\n bucket 26: 50%\n bucket 25: 60%\n bucket 26: 60%\n bucket 25: 70%\n bucket 26: 70%\n bucket 25: 80%\n bucket 26: 80%\n bucket 25: 90%\n bucket 26: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 27 of 29\nGetting block 28 of 29\n Reserving size (252) for bucket 27\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 27\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 28:\n bucket 27: 10%\n bucket 28: 10%\n bucket 27: 20%\n bucket 28: 20%\n bucket 27: 30%\n bucket 28: 30%\n bucket 27: 40%\n bucket 28: 40%\n bucket 28: 50%\n bucket 27: 50%\n bucket 28: 60%\n bucket 27: 60%\n bucket 28: 70%\n bucket 27: 70%\n bucket 28: 80%\n bucket 27: 80%\n bucket 28: 90%\n bucket 27: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\nGetting block 3 of 29\n Entering block accumulator loop for bucket 1:\n Reserving size (252) for bucket 3\n Reserving size (252) for bucket 2\nGetting block 4 of 29\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 2\n bucket 1: 10%\n Reserving size (252) for bucket 4\n bucket 1: 20%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 2:\n bucket 3: 10%\n bucket 1: 30%\n bucket 3: 20%\n bucket 2: 10%\n bucket 3: 30%\n bucket 1: 40%\n Entering block accumulator loop for bucket 4:\n bucket 2: 20%\n bucket 1: 50%\n bucket 3: 40%\n bucket 4: 10%\n bucket 1: 60%\n bucket 3: 50%\n bucket 2: 30%\n bucket 1: 70%\n bucket 4: 20%\n bucket 3: 60%\n bucket 1: 80%\n bucket 2: 40%\n bucket 4: 30%\n bucket 3: 70%\n bucket 1: 90%\n bucket 2: 50%\n bucket 4: 40%\n bucket 3: 80%\n bucket 2: 60%\n bucket 1: 100%\n bucket 4: 50%\n Sorting block of length 127 for bucket 1\n bucket 3: 90%\n bucket 2: 70%\n (Using difference cover)\n bucket 4: 60%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 2: 80%\n bucket 4: 70%\n bucket 2: 90%\n bucket 4: 80%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n bucket 4: 90%\n (Using difference cover)\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 6:\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\nGetting block 8 of 29\n bucket 7: 10%\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n bucket 7: 20%\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 7: 30%\n bucket 8: 20%\n bucket 7: 40%\n bucket 7: 50%\n bucket 8: 30%\n bucket 7: 60%\n bucket 8: 40%\n bucket 7: 70%\n bucket 8: 50%\n bucket 7: 80%\n bucket 8: 60%\n bucket 7: 90%\n bucket 8: 70%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 9\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 9: 50%\n bucket 10: 50%\n bucket 9: 60%\n bucket 10: 60%\n bucket 10: 70%\n bucket 9: 70%\n bucket 10: 80%\n bucket 9: 80%\n bucket 10: 90%\n bucket 9: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 11 of 29\n Reserving size (252) for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 11:\n bucket 12: 10%\n bucket 11: 10%\n bucket 12: 20%\n bucket 11: 20%\n bucket 12: 30%\n bucket 11: 30%\n bucket 12: 40%\n bucket 11: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 11: 50%\n bucket 12: 70%\n bucket 11: 60%\n bucket 12: 80%\n bucket 11: 70%\n bucket 12: 90%\n bucket 11: 80%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 13 of 29\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 14\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 13:\n bucket 14: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 13: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 13: 30%\n bucket 14: 50%\n bucket 13: 40%\n bucket 14: 60%\n bucket 13: 50%\n bucket 14: 70%\n bucket 13: 60%\n bucket 14: 80%\n bucket 14: 90%\n bucket 13: 70%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n bucket 13: 80%\n (Using difference cover)\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Entering block accumulator loop for bucket 15:\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 16: 20%\n bucket 15: 40%\n bucket 16: 30%\n bucket 15: 50%\n bucket 16: 40%\n bucket 15: 60%\n bucket 16: 50%\n bucket 15: 70%\n bucket 16: 60%\n bucket 15: 80%\n bucket 16: 70%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n bucket 16: 80%\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n Entering block accumulator loop for bucket 20:\n bucket 19: 10%\n bucket 20: 10%\n bucket 19: 20%\n bucket 20: 20%\n bucket 19: 30%\n bucket 20: 30%\n bucket 19: 40%\n bucket 20: 40%\n bucket 19: 50%\n bucket 20: 50%\n bucket 19: 60%\n bucket 20: 60%\n bucket 19: 70%\n bucket 20: 70%\n bucket 19: 80%\n bucket 20: 80%\n bucket 19: 90%\n bucket 20: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\nGetting block 26 of 29\n Calculating Z arrays for bucket 25\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 26:\n bucket 25: 10%\n bucket 26: 10%\n bucket 25: 20%\n bucket 26: 20%\n bucket 25: 30%\n bucket 26: 30%\n bucket 25: 40%\n bucket 26: 40%\n bucket 25: 50%\n bucket 26: 50%\n bucket 25: 60%\n bucket 26: 60%\n bucket 25: 70%\n bucket 26: 70%\n bucket 25: 80%\n bucket 26: 80%\n bucket 25: 90%\n bucket 26: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 27 of 29\nGetting block 28 of 29\n Reserving size (252) for bucket 27\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 27\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 28:\n bucket 27: 10%\n bucket 28: 10%\n bucket 27: 20%\n bucket 28: 20%\n bucket 27: 30%\n bucket 28: 30%\n bucket 27: 40%\n bucket 28: 40%\n bucket 28: 50%\n bucket 27: 50%\n bucket 28: 60%\n bucket 27: 60%\n bucket 28: 70%\n bucket 27: 70%\n bucket 28: 80%\n bucket 27: 80%\n bucket 28: 90%\n bucket 27: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\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": "2023-10-24 15:25:58", "plugin": "core", "name": "end_epoch", "raw_value": "1698161158.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:25:57", "plugin": "core", "name": "start_epoch", "raw_value": "1698161157.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-2", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 2, "time_seconds": 152.77250337600708, "inputs": {"reference_genome|source": "indexed", "library|input_1": {"src": "hda", "id": "23cecfd7c89355b4"}, "library|input_2": {"src": "hda", "id": "b32413f4a3e2c242"}, "library|type": "paired"}, "job": {"model_class": "Job", "id": "739cf057da645fe3", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:54:14.600478", "create_time": "2023-10-24T14:51:53.145973", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-dz684", "command_line": "set -o pipefail; ln -f -s '/galaxy/server/database/objects/9/a/3/dataset_9a3338d4-895a-4c16-bdfa-01bc6cb21576.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/a/1/9/dataset_a19a6d27-64c0-496f-8cac-0d633ca3c455.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x '/cvmfs/data.galaxyproject.org/managed/hisat2_index/apiMel4/apiMel4' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/a/2/5/dataset_a25c5794-45a5-4324-aa24-8aae26b61d36.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"phiX\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/phiX.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 185, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 186, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 0, \"index\": \"apiMel4\", \"source\": \"indexed\"}"}, "inputs": {"input_1": {"id": "23cecfd7c89355b4", "src": "hda", "uuid": "9a3338d4-895a-4c16-bdfa-01bc6cb21576"}, "input_2": {"id": "b32413f4a3e2c242", "src": "hda", "uuid": "a19a6d27-64c0-496f-8cac-0d633ca3c455"}}, "outputs": {"output_alignments": {"id": "c71f60e8232c1291", "src": "hda", "uuid": "a25c5794-45a5-4324-aa24-8aae26b61d36"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "10 reads; of these:\n 10 (100.00%) were paired; of these:\n 10 (100.00%) aligned concordantly 0 times\n 0 (0.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 10 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 10 pairs aligned 0 times concordantly or discordantly; of these:\n 20 mates make up the pairs; of these:\n 20 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "stderr": "\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 10 (100.00%) aligned concordantly 0 times\n 0 (0.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 10 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 10 pairs aligned 0 times concordantly or discordantly; of these:\n 20 mates make up the pairs; of these:\n 20 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "21 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "21.0000000"}, {"title": "Job End Time", "value": "2023-10-24 14:54:04", "plugin": "core", "name": "end_epoch", "raw_value": "1698159244.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:53:43", "plugin": "core", "name": "start_epoch", "raw_value": "1698159223.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "output_problems": ["Output output_alignments: different than expected, difference (using diff):\n( /tmp/local_bam_converted_to_sam_4nxwajj6.sam v. /tmp/history_bam_converted_to_sam_7jvtfoxr.sam )\n--- local_file\n+++ history_data\n@@ -1,23 +1,5343 @@\n @HD\tVN:1.0\tSO:coordinate\n-@PG\tID:hisat2\tPN:hisat2\tVN:2.1.0\tCL:\"/home/maria/miniconda3/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin/hisat2-align-s --wrapper basic-0 -p 1 -x genome -1 input_f.fastq -2 input_r.fastq\"\n-@SQ\tSN:phiX174\tLN:5386\n-phiX174_1141_1609_1:0:0_1:0:0_4\t147\tphiX174\t1540\t60\t70M\t=\t1141\t-469\tTTCTAGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tZS:i:-5\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:4C65\tYS:i:-3\tYT:Z:CP\tNH:i:1\n-phiX174_1141_1609_1:0:0_1:0:0_4\t99\tphiX174\t1141\t60\t70M\t=\t1540\t469\tTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:24G45\tYS:i:-3\tYT:Z:CP\tNH:i:1\n-phiX174_1363_1914_3:0:0_0:0:0_6\t133\tphiX174\t1845\t0\t*\t=\t1845\t0\tTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAGCGCCGAGGATGCGTGACCGT\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n-phiX174_1363_1914_3:0:0_0:0:0_6\t89\tphiX174\t1845\t60\t70M\t=\t1845\t0\tGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGC\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYT:Z:UP\tNH:i:1\n-phiX174_1542_1965_0:0:0_0:0:0_1\t147\tphiX174\t1896\t60\t70M\t=\t1542\t-424\tAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:0\tYT:Z:CP\tNH:i:1\n-phiX174_1542_1965_0:0:0_0:0:0_1\t99\tphiX174\t1542\t60\t70M\t=\t1896\t424\tCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:0\tYT:Z:CP\tNH:i:1\n-phiX174_185_708_0:0:0_1:0:0_5\t147\tphiX174\t639\t60\t70M\t=\t185\t-524\tTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCGCATCATGGAAGGCGCTGAATTTACGGAAAACA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:37T32\tYS:i:0\tYT:Z:CP\tNH:i:1\n-phiX174_185_708_0:0:0_1:0:0_5\t99\tphiX174\t185\t60\t70M\t=\t639\t524\tCCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:-3\tYT:Z:CP\tNH:i:1\n-phiX174_1980_2501_0:1:0_3:0:0_0\t163\tphiX174\t1980\t60\t70M\t=\t2432\t522\tGTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:12T57\tYS:i:-9\tYT:Z:CP\tNH:i:1\n-phiX174_1980_2501_0:1:0_3:0:0_0\t83\tphiX174\t2432\t60\t70M\t=\t1980\t-522\tTTTTTTCTGATAAGCTGGTTCTCAATTCTGTTAATCCAGCTTCTTCGGCACCTGTTTTACACACACCTAA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-9\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:24C8C27G8\tYS:i:-3\tYT:Z:CP\tNH:i:1\n-phiX174_2128_2577_0:0:0_4:0:0_9\t147\tphiX174\t2508\t60\t70M\t=\t2128\t-450\tATCGTCAACGTTATATTTTGATAGTTTGAAGGTTAATGCTGGTATTGGTGGTTTTCTTAATTCCATTCAG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-12\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:29C14A13C3G7\tYS:i:0\tYT:Z:CP\tNH:i:1\n-phiX174_2128_2577_0:0:0_4:0:0_9\t99\tphiX174\t2128\t60\t70M\t=\t2508\t450\tTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:-12\tYT:Z:CP\tNH:i:1\n-phiX174_2259_2739_1:0:0_1:0:0_3\t147\tphiX174\t2670\t60\t70M\t=\t2259\t-481\tTCGCTTTGAGTCTTCGTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGC\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:15T54\tYS:i:-2\tYT:Z:CP\tNH:i:1\n-phiX174_2259_2739_1:0:0_1:0:0_3\t99\tphiX174\t2259\t60\t68M2S\t=\t2670\t481\tCTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAAAT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-2\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:68\tYS:i:-3\tYT:Z:CP\tNH:i:1\n-phiX174_2950_3377_0:0:0_2:0:0_2\t163\tphiX174\t2950\t60\t70M\t=\t3308\t428\tGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTC\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:-6\tYT:Z:CP\tNH:i:1\n-phiX174_2950_3377_0:0:0_2:0:0_2\t83\tphiX174\t3308\t60\t70M\t=\t2950\t-428\tTGAGATTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTATGCTGGTATGGTTGACGCCGGATTTGAG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-6\tZS:i:-8\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:4C36C28\tYS:i:0\tYT:Z:CP\tNH:i:1\n-phiX174_3199_3732_0:0:0_1:0:0_7\t147\tphiX174\t3663\t60\t70M\t=\t3199\t-534\tAATGACCAAATCAATGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:14A55\tYS:i:0\tYT:Z:CP\tNH:i:1\n-phiX174_3199_3732_0:0:0_1:0:0_7\t99\tphiX174\t3199\t60\t70M\t=\t3663\t534\tCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:-3\tYT:Z:CP\tNH:i:1\n-phiX174_36_572_1:0:0_0:0:0_8\t163\tphiX174\t36\t60\t70M\t=\t503\t537\tTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATTACTACTGCTTGTTTACGAAT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:45G24\tYS:i:0\tYT:Z:CP\tNH:i:1\n********\n*SNIP *\n********\n+@SQ\tSN:Group6\tLN:18472937\n+@SQ\tSN:Group7\tLN:13219345\n+@SQ\tSN:Group8\tLN:13546544\n+@SQ\tSN:Group9\tLN:11120453\n+@SQ\tSN:chrM\tLN:16343\n+phiX174_1141_1609_1:0:0_1:0:0_4\t141\t*\t0\t0\t*\t*\t0\t0\tCAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCTAGAA\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_1141_1609_1:0:0_1:0:0_4\t77\t*\t0\t0\t*\t*\t0\t0\tTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTT\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_1363_1914_3:0:0_0:0:0_6\t141\t*\t0\t0\t*\t*\t0\t0\tTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAGCGCCGAGGATGCGTGACCGT\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_1363_1914_3:0:0_0:0:0_6\t77\t*\t0\t0\t*\t*\t0\t0\tGCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGC\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_1542_1965_0:0:0_0:0:0_1\t141\t*\t0\t0\t*\t*\t0\t0\tCCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCT\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_1542_1965_0:0:0_0:0:0_1\t77\t*\t0\t0\t*\t*\t0\t0\tCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_185_708_0:0:0_1:0:0_5\t141\t*\t0\t0\t*\t*\t0\t0\tTGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATGTTGACGGGATGAACATAATA\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_185_708_0:0:0_1:0:0_5\t77\t*\t0\t0\t*\t*\t0\t0\tCCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCT\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_1980_2501_0:1:0_3:0:0_0\t141\t*\t0\t0\t*\t*\t0\t0\tGTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCA\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_1980_2501_0:1:0_3:0:0_0\t77\t*\t0\t0\t*\t*\t0\t0\tTTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAGAACCAGCTTATCAGAAAAAA\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_2128_2577_0:0:0_4:0:0_9\t141\t*\t0\t0\t*\t*\t0\t0\tCTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTATCAAAATATAACGTTGACGAT\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_2128_2577_0:0:0_4:0:0_9\t77\t*\t0\t0\t*\t*\t0\t0\tTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAG\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_2259_2739_1:0:0_1:0:0_3\t141\t*\t0\t0\t*\t*\t0\t0\tGCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCGACGAAGACTCAAAGCGA\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_2259_2739_1:0:0_1:0:0_3\t77\t*\t0\t0\t*\t*\t0\t0\tCTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAAAT\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_2950_3377_0:0:0_2:0:0_2\t141\t*\t0\t0\t*\t*\t0\t0\tGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTC\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_2950_3377_0:0:0_2:0:0_2\t77\t*\t0\t0\t*\t*\t0\t0\tCTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAATCTCA\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_3199_3732_0:0:0_1:0:0_7\t141\t*\t0\t0\t*\t*\t0\t0\tTCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTCATTTCATTGATTTGGTCATT\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_3199_3732_0:0:0_1:0:0_7\t77\t*\t0\t0\t*\t*\t0\t0\tCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAA\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_36_572_1:0:0_0:0:0_8\t141\t*\t0\t0\t*\t*\t0\t0\tTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATTACTACTGCTTGTTTACGAAT\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_36_572_1:0:0_0:0:0_8\t77\t*\t0\t0\t*\t*\t0\t0\tACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTC\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n"], "status": "failure"}}, {"id": "hisat2/2.2.1+galaxy1-3", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 3, "time_seconds": 139.76000142097473, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "a3a22eb3384f632c"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "49029730a07a2de5"}, "library|input_2": {"src": "hda", "id": "273c1023f647f01a"}, "library|type": "paired", "adv|input_options|trim5": "15", "adv|input_options|trim3": "15", "adv|input_options|input_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "ad40023effa91a45", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:56:33.994643", "create_time": "2023-10-24T14:54:32.704958", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-pf5d8", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/4/1/3/dataset_413901b1-3f2f-4dc2-9170-53888d1c5182.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/0/3/b/dataset_03ba2680-70f3-477a-9d58-66be64d23638.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/a/4/c/dataset_a4cb6c26-3dde-44fc-a41d-c0a3dc7e440c.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' --trim5 '15' --trim3 '15' --phred33 | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/5/4/3/dataset_54360dfa-1206-4bcf-ac8a-e62b755aa236.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 1, \"input_options_selector\": \"advanced\", \"int_quals\": \"false\", \"qupto\": \"0\", \"qv_encoding\": \"--phred33\", \"skip\": \"0\", \"solexa_quals\": \"false\", \"trim3\": \"15\", \"trim5\": \"15\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 189, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 190, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 188, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "a3a22eb3384f632c", "src": "hda", "uuid": "413901b1-3f2f-4dc2-9170-53888d1c5182"}, "input_1": {"id": "49029730a07a2de5", "src": "hda", "uuid": "03ba2680-70f3-477a-9d58-66be64d23638"}, "input_2": {"id": "273c1023f647f01a", "src": "hda", "uuid": "a4cb6c26-3dde-44fc-a41d-c0a3dc7e440c"}}, "outputs": {"output_alignments": {"id": "230ab0a958c21eee", "src": "hda", "uuid": "54360dfa-1206-4bcf-ac8a-e62b755aa236"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\n bucket 1: 20%\n bucket 1: 30%\n bucket 1: 40%\n bucket 1: 50%\nGetting block 2 of 29\n bucket 1: 60%\n Reserving size (252) for bucket 2\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n bucket 1: 70%\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 2\n bucket 1: 80%\nGetting block 3 of 29\n Entering block accumulator loop for bucket 4:\n Reserving size (252) for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 90%\n Calculating Z arrays for bucket 3\n bucket 2: 10%\n bucket 1: 100%\n bucket 4: 10%\n Sorting block of length 127 for bucket 1\n bucket 2: 20%\n (Using difference cover)\n Entering block accumulator loop for bucket 3:\n bucket 4: 20%\n bucket 2: 30%\n bucket 3: 10%\n bucket 4: 30%\n bucket 2: 40%\n bucket 3: 20%\n bucket 4: 40%\n bucket 2: 50%\n bucket 3: 30%\n bucket 4: 50%\n bucket 2: 60%\n bucket 3: 40%\n bucket 4: 60%\n bucket 2: 70%\n bucket 3: 50%\n bucket 4: 70%\n bucket 2: 80%\n bucket 3: 60%\n bucket 4: 80%\n bucket 2: 90%\n bucket 3: 70%\n bucket 4: 90%\n bucket 2: 100%\n bucket 3: 80%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n bucket 3: 90%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\nGetting block 7 of 29\n bucket 5: 10%\n Reserving size (252) for bucket 7\n Entering block accumulator loop for bucket 6:\n Calculating Z arrays for bucket 7\n bucket 5: 20%\n bucket 6: 10%\n bucket 5: 30%\n Entering block accumulator loop for bucket 7:\n bucket 6: 20%\n bucket 5: 40%\n bucket 6: 30%\n bucket 7: 10%\n bucket 5: 50%\n bucket 6: 40%\n bucket 5: 60%\n bucket 7: 20%\n bucket 6: 50%\n bucket 5: 70%\n bucket 7: 30%\n bucket 6: 60%\n bucket 5: 80%\n bucket 7: 40%\n bucket 5: 90%\n bucket 6: 70%\n bucket 7: 50%\n bucket 5: 100%\n bucket 6: 80%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 7: 60%\n bucket 6: 90%\n bucket 7: 70%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n bucket 9: 90%\n Calculating Z arrays for bucket 10\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 13:\n bucket 14: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 13: 20%\n bucket 14: 30%\n bucket 13: 30%\n bucket 14: 40%\n bucket 13: 40%\n bucket 14: 50%\n bucket 13: 50%\n bucket 14: 60%\n bucket 13: 60%\n bucket 14: 70%\n bucket 13: 70%\n bucket 14: 80%\n bucket 13: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\nGetting block 18 of 29\n bucket 17: 60%\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 70%\n Entering block accumulator loop for bucket 18:\n bucket 17: 80%\n bucket 18: 10%\n bucket 17: 90%\n bucket 18: 20%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n Entering block accumulator loop for bucket 20:\n (Using difference cover)\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 22:\n Entering block accumulator loop for bucket 21:\n bucket 22: 10%\n bucket 21: 10%\n bucket 22: 20%\n bucket 21: 20%\n bucket 22: 30%\n bucket 21: 30%\n bucket 22: 40%\n bucket 21: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 21: 50%\n bucket 22: 70%\n bucket 21: 60%\n bucket 22: 80%\n bucket 21: 70%\n bucket 22: 90%\n bucket 21: 80%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n bucket 21: 90%\n (Using difference cover)\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n Calculating Z arrays for bucket 25\n bucket 26: 30%\n Entering block accumulator loop for bucket 25:\n bucket 26: 40%\n bucket 25: 10%\n bucket 26: 50%\n bucket 25: 20%\n bucket 26: 60%\n bucket 25: 30%\n bucket 26: 70%\n bucket 25: 40%\n bucket 26: 80%\n bucket 25: 50%\n bucket 26: 90%\n bucket 25: 60%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n bucket 25: 70%\n bucket 25: 80%\n (Using difference cover)\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n Sorting block time: 00:00:00\n bucket 28: 60%\nReturning block of 234 for bucket 27\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 71 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 71 pairs aligned 0 times concordantly or discordantly; of these:\n 142 mates make up the pairs; of these:\n 74 (52.11%) aligned 0 times\n 68 (47.89%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n92.60% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 71 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 71 pairs aligned 0 times concordantly or discordantly; of these:\n 142 mates make up the pairs; of these:\n 74 (52.11%) aligned 0 times\n 68 (47.89%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n92.60% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\n bucket 1: 20%\n bucket 1: 30%\n bucket 1: 40%\n bucket 1: 50%\nGetting block 2 of 29\n bucket 1: 60%\n Reserving size (252) for bucket 2\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n bucket 1: 70%\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 2\n bucket 1: 80%\nGetting block 3 of 29\n Entering block accumulator loop for bucket 4:\n Reserving size (252) for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 90%\n Calculating Z arrays for bucket 3\n bucket 2: 10%\n bucket 1: 100%\n bucket 4: 10%\n Sorting block of length 127 for bucket 1\n bucket 2: 20%\n (Using difference cover)\n Entering block accumulator loop for bucket 3:\n bucket 4: 20%\n bucket 2: 30%\n bucket 3: 10%\n bucket 4: 30%\n bucket 2: 40%\n bucket 3: 20%\n bucket 4: 40%\n bucket 2: 50%\n bucket 3: 30%\n bucket 4: 50%\n bucket 2: 60%\n bucket 3: 40%\n bucket 4: 60%\n bucket 2: 70%\n bucket 3: 50%\n bucket 4: 70%\n bucket 2: 80%\n bucket 3: 60%\n bucket 4: 80%\n bucket 2: 90%\n bucket 3: 70%\n bucket 4: 90%\n bucket 2: 100%\n bucket 3: 80%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n bucket 3: 90%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\nGetting block 7 of 29\n bucket 5: 10%\n Reserving size (252) for bucket 7\n Entering block accumulator loop for bucket 6:\n Calculating Z arrays for bucket 7\n bucket 5: 20%\n bucket 6: 10%\n bucket 5: 30%\n Entering block accumulator loop for bucket 7:\n bucket 6: 20%\n bucket 5: 40%\n bucket 6: 30%\n bucket 7: 10%\n bucket 5: 50%\n bucket 6: 40%\n bucket 5: 60%\n bucket 7: 20%\n bucket 6: 50%\n bucket 5: 70%\n bucket 7: 30%\n bucket 6: 60%\n bucket 5: 80%\n bucket 7: 40%\n bucket 5: 90%\n bucket 6: 70%\n bucket 7: 50%\n bucket 5: 100%\n bucket 6: 80%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 7: 60%\n bucket 6: 90%\n bucket 7: 70%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n bucket 9: 90%\n Calculating Z arrays for bucket 10\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 13:\n bucket 14: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 13: 20%\n bucket 14: 30%\n bucket 13: 30%\n bucket 14: 40%\n bucket 13: 40%\n bucket 14: 50%\n bucket 13: 50%\n bucket 14: 60%\n bucket 13: 60%\n bucket 14: 70%\n bucket 13: 70%\n bucket 14: 80%\n bucket 13: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\nGetting block 18 of 29\n bucket 17: 60%\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 70%\n Entering block accumulator loop for bucket 18:\n bucket 17: 80%\n bucket 18: 10%\n bucket 17: 90%\n bucket 18: 20%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n Entering block accumulator loop for bucket 20:\n (Using difference cover)\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 22:\n Entering block accumulator loop for bucket 21:\n bucket 22: 10%\n bucket 21: 10%\n bucket 22: 20%\n bucket 21: 20%\n bucket 22: 30%\n bucket 21: 30%\n bucket 22: 40%\n bucket 21: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 21: 50%\n bucket 22: 70%\n bucket 21: 60%\n bucket 22: 80%\n bucket 21: 70%\n bucket 22: 90%\n bucket 21: 80%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n bucket 21: 90%\n (Using difference cover)\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n Calculating Z arrays for bucket 25\n bucket 26: 30%\n Entering block accumulator loop for bucket 25:\n bucket 26: 40%\n bucket 25: 10%\n bucket 26: 50%\n bucket 25: 20%\n bucket 26: 60%\n bucket 25: 30%\n bucket 26: 70%\n bucket 25: 40%\n bucket 26: 80%\n bucket 25: 50%\n bucket 26: 90%\n bucket 25: 60%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n bucket 25: 70%\n bucket 25: 80%\n (Using difference cover)\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n Sorting block time: 00:00:00\n bucket 28: 60%\nReturning block of 234 for bucket 27\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "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": "2023-10-24 14:56:24", "plugin": "core", "name": "end_epoch", "raw_value": "1698159384.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:56:24", "plugin": "core", "name": "start_epoch", "raw_value": "1698159384.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-4", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 4, "time_seconds": 142.19959211349487, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "6fcf1231f0877472"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "c3d995c6e58f4716"}, "library|input_2": {"src": "hda", "id": "9100a0deb5eb8a25"}, "library|paired_options|no_mixed": true, "library|paired_options|no_discordant": true, "library|paired_options|paired_options_selector": "advanced", "library|type": "paired", "adv|input_options|trim5": "15", "adv|input_options|trim3": "15", "adv|input_options|input_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "644661f6f911b6a8", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:58:56.143147", "create_time": "2023-10-24T14:56:51.298269", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-8j2zh", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/0/8/d/dataset_08d1d5b5-3796-43b2-bb6b-352b5523af56.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/d/0/6/dataset_d063568d-1376-49f3-898a-3b32f6a0a6f9.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/e/1/a/dataset_e1ad5c67-594b-43ba-b47a-9a2791c13b91.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' --fr --no-mixed --no-discordant --trim5 '15' --trim3 '15' --phred33 | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/9/a/5/dataset_9a59e79a-f800-46a5-8fab-1a2727c77e84.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 1, \"input_options_selector\": \"advanced\", \"int_quals\": \"false\", \"qupto\": \"0\", \"qv_encoding\": \"--phred33\", \"skip\": \"0\", \"solexa_quals\": \"false\", \"trim3\": \"15\", \"trim5\": \"15\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 193, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 194, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"fr_rf_ff\": \"--fr\", \"no_discordant\": \"true\", \"no_mixed\": \"true\", \"paired_options_selector\": \"advanced\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 192, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "6fcf1231f0877472", "src": "hda", "uuid": "08d1d5b5-3796-43b2-bb6b-352b5523af56"}, "input_1": {"id": "c3d995c6e58f4716", "src": "hda", "uuid": "d063568d-1376-49f3-898a-3b32f6a0a6f9"}, "input_2": {"id": "9100a0deb5eb8a25", "src": "hda", "uuid": "e1ad5c67-594b-43ba-b47a-9a2791c13b91"}}, "outputs": {"output_alignments": {"id": "2abb767e6f461629", "src": "hda", "uuid": "9a59e79a-f800-46a5-8fab-1a2727c77e84"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\nGetting block 2 of 29\n Reserving size (252) for bucket 2\n bucket 1: 20%\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n bucket 1: 30%\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 2\n bucket 1: 40%\n bucket 1: 50%\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 2:\n bucket 1: 60%\n Calculating Z arrays for bucket 4\n bucket 2: 10%\n bucket 3: 10%\n bucket 1: 70%\n bucket 2: 20%\n bucket 3: 20%\n Entering block accumulator loop for bucket 4:\n bucket 1: 80%\n bucket 2: 30%\n bucket 3: 30%\n bucket 1: 90%\n bucket 4: 10%\n bucket 2: 40%\n bucket 3: 40%\n bucket 1: 100%\n bucket 4: 20%\n Sorting block of length 127 for bucket 1\n bucket 2: 50%\n (Using difference cover)\n bucket 3: 50%\n bucket 4: 30%\n bucket 2: 60%\n bucket 3: 60%\n bucket 4: 40%\n bucket 2: 70%\n bucket 3: 70%\n bucket 4: 50%\n bucket 2: 80%\n bucket 3: 80%\n bucket 4: 60%\n bucket 2: 90%\n bucket 3: 90%\n bucket 4: 70%\n bucket 2: 100%\n bucket 3: 100%\n Sorting block of length 239 for bucket 2\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 4: 80%\n (Using difference cover)\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n Calculating Z arrays for bucket 6\n bucket 5: 60%\n bucket 5: 70%\n Entering block accumulator loop for bucket 6:\n bucket 5: 80%\n bucket 6: 10%\n bucket 5: 90%\n bucket 6: 20%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n bucket 7: 70%\n Calculating Z arrays for bucket 8\n bucket 7: 80%\n Entering block accumulator loop for bucket 8:\n bucket 7: 90%\n bucket 8: 10%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Entering block accumulator loop for bucket 9:\n Calculating Z arrays for bucket 10\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 9: 30%\n bucket 10: 80%\n bucket 9: 40%\n bucket 10: 90%\n bucket 9: 50%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\nGetting block 15 of 29\n bucket 14: 50%\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 60%\n bucket 14: 70%\n Entering block accumulator loop for bucket 15:\n bucket 14: 80%\n bucket 14: 90%\n bucket 15: 10%\n bucket 14: 100%\n bucket 15: 20%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 40%\n bucket 18: 50%\n Entering block accumulator loop for bucket 19:\n bucket 18: 60%\n bucket 19: 10%\n bucket 18: 70%\n bucket 18: 80%\n bucket 19: 20%\n bucket 18: 90%\n bucket 19: 30%\n bucket 19: 40%\n bucket 18: 100%\n bucket 19: 50%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Entering block accumulator loop for bucket 22:\n Calculating Z arrays for bucket 23\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 22: 50%\n bucket 23: 40%\n bucket 23: 50%\n bucket 22: 60%\n bucket 23: 60%\n bucket 22: 70%\n bucket 23: 70%\n bucket 22: 80%\n bucket 23: 80%\n bucket 22: 90%\n bucket 23: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 29\n Entering block accumulator loop for bucket 26:\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 10%\n Entering block accumulator loop for bucket 27:\n bucket 26: 20%\n bucket 27: 10%\n bucket 26: 30%\n bucket 27: 20%\n bucket 26: 40%\n bucket 27: 30%\n bucket 26: 50%\n bucket 27: 40%\n bucket 26: 60%\n bucket 27: 50%\n bucket 26: 70%\n bucket 27: 60%\n bucket 26: 80%\n bucket 27: 70%\n bucket 26: 90%\n bucket 27: 80%\n bucket 26: 100%\n bucket 27: 90%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 28:\n bucket 29: 10%\n bucket 29: 20%\n bucket 28: 10%\n bucket 29: 30%\n bucket 28: 20%\n bucket 29: 40%\n bucket 28: 30%\n bucket 29: 50%\n bucket 28: 40%\n bucket 29: 60%\n bucket 29: 70%\n bucket 28: 50%\n bucket 29: 80%\n bucket 28: 60%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\nGetting block 2 of 29\n Reserving size (252) for bucket 2\n bucket 1: 20%\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n bucket 1: 30%\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 2\n bucket 1: 40%\n bucket 1: 50%\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 2:\n bucket 1: 60%\n Calculating Z arrays for bucket 4\n bucket 2: 10%\n bucket 3: 10%\n bucket 1: 70%\n bucket 2: 20%\n bucket 3: 20%\n Entering block accumulator loop for bucket 4:\n bucket 1: 80%\n bucket 2: 30%\n bucket 3: 30%\n bucket 1: 90%\n bucket 4: 10%\n bucket 2: 40%\n bucket 3: 40%\n bucket 1: 100%\n bucket 4: 20%\n Sorting block of length 127 for bucket 1\n bucket 2: 50%\n (Using difference cover)\n bucket 3: 50%\n bucket 4: 30%\n bucket 2: 60%\n bucket 3: 60%\n bucket 4: 40%\n bucket 2: 70%\n bucket 3: 70%\n bucket 4: 50%\n bucket 2: 80%\n bucket 3: 80%\n bucket 4: 60%\n bucket 2: 90%\n bucket 3: 90%\n bucket 4: 70%\n bucket 2: 100%\n bucket 3: 100%\n Sorting block of length 239 for bucket 2\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 4: 80%\n (Using difference cover)\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n Calculating Z arrays for bucket 6\n bucket 5: 60%\n bucket 5: 70%\n Entering block accumulator loop for bucket 6:\n bucket 5: 80%\n bucket 6: 10%\n bucket 5: 90%\n bucket 6: 20%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n bucket 7: 70%\n Calculating Z arrays for bucket 8\n bucket 7: 80%\n Entering block accumulator loop for bucket 8:\n bucket 7: 90%\n bucket 8: 10%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Entering block accumulator loop for bucket 9:\n Calculating Z arrays for bucket 10\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 9: 30%\n bucket 10: 80%\n bucket 9: 40%\n bucket 10: 90%\n bucket 9: 50%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\nGetting block 15 of 29\n bucket 14: 50%\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 60%\n bucket 14: 70%\n Entering block accumulator loop for bucket 15:\n bucket 14: 80%\n bucket 14: 90%\n bucket 15: 10%\n bucket 14: 100%\n bucket 15: 20%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 40%\n bucket 18: 50%\n Entering block accumulator loop for bucket 19:\n bucket 18: 60%\n bucket 19: 10%\n bucket 18: 70%\n bucket 18: 80%\n bucket 19: 20%\n bucket 18: 90%\n bucket 19: 30%\n bucket 19: 40%\n bucket 18: 100%\n bucket 19: 50%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Entering block accumulator loop for bucket 22:\n Calculating Z arrays for bucket 23\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 22: 50%\n bucket 23: 40%\n bucket 23: 50%\n bucket 22: 60%\n bucket 23: 60%\n bucket 22: 70%\n bucket 23: 70%\n bucket 22: 80%\n bucket 23: 80%\n bucket 22: 90%\n bucket 23: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 29\n Entering block accumulator loop for bucket 26:\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 10%\n Entering block accumulator loop for bucket 27:\n bucket 26: 20%\n bucket 27: 10%\n bucket 26: 30%\n bucket 27: 20%\n bucket 26: 40%\n bucket 27: 30%\n bucket 26: 50%\n bucket 27: 40%\n bucket 26: 60%\n bucket 27: 50%\n bucket 26: 70%\n bucket 27: 60%\n bucket 26: 80%\n bucket 27: 70%\n bucket 26: 90%\n bucket 27: 80%\n bucket 26: 100%\n bucket 27: 90%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 28:\n bucket 29: 10%\n bucket 29: 20%\n bucket 28: 10%\n bucket 29: 30%\n bucket 28: 20%\n bucket 29: 40%\n bucket 28: 30%\n bucket 29: 50%\n bucket 28: 40%\n bucket 29: 60%\n bucket 29: 70%\n bucket 28: 50%\n bucket 29: 80%\n bucket 28: 60%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\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": "2023-10-24 14:58:47", "plugin": "core", "name": "end_epoch", "raw_value": "1698159527.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:58:46", "plugin": "core", "name": "start_epoch", "raw_value": "1698159526.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-5", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 5, "time_seconds": 135.2423403263092, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "2439f88eb1dff570"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "6b02307edce0a4e6"}, "library|type": "single", "adv|output_options|unaligned_file": true, "adv|output_options|output_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "ae1b404e546d0479", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:01:11.797248", "create_time": "2023-10-24T14:59:07.824364", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-9d8p4", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/2/e/f/dataset_2efe48c0-4d13-43c9-94af-60be891bb8d1.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/7/1/a/dataset_71a9d36d-e035-4962-8058-62ef3696fcd0.dat' input_f.fasta && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -f -U 'input_f.fasta' --un '/galaxy/server/database/objects/d/a/a/dataset_daa2883b-30ed-481c-b51f-eb5f6cf18710.dat' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/7/0/7/dataset_707935b6-82d1-409a-973c-84fbd4b74792.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 1, \"aligned_file\": \"false\", \"output_options_selector\": \"advanced\", \"unaligned_file\": \"true\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 197, \"src\": \"hda\"}]}, \"rna_strandness\": \"\", \"type\": \"single\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 196, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "2439f88eb1dff570", "src": "hda", "uuid": "2efe48c0-4d13-43c9-94af-60be891bb8d1"}, "input_1": {"id": "6b02307edce0a4e6", "src": "hda", "uuid": "71a9d36d-e035-4962-8058-62ef3696fcd0"}}, "outputs": {"output_alignments": {"id": "37f8a368e0913024", "src": "hda", "uuid": "707935b6-82d1-409a-973c-84fbd4b74792"}, "output_unaligned_reads_l": {"id": "13593664e49e10f8", "src": "hda", "uuid": "daa2883b-30ed-481c-b51f-eb5f6cf18710"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\nGetting block 2 of 29\n Reserving size (252) for bucket 2\nGetting block 3 of 29\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n Reserving size (252) for bucket 3\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 3:\n bucket 1: 10%\n bucket 4: 10%\n bucket 2: 10%\n bucket 1: 20%\n bucket 4: 20%\n bucket 3: 10%\n bucket 2: 20%\n bucket 1: 30%\n bucket 4: 30%\n bucket 3: 20%\n bucket 2: 30%\n bucket 1: 40%\n bucket 4: 40%\n bucket 2: 40%\n bucket 1: 50%\n bucket 4: 50%\n bucket 2: 50%\n bucket 1: 60%\n bucket 3: 30%\n bucket 2: 60%\n bucket 1: 70%\n bucket 3: 40%\n bucket 4: 60%\n bucket 1: 80%\n bucket 2: 70%\n bucket 3: 50%\n bucket 4: 70%\n bucket 1: 90%\n bucket 3: 60%\n bucket 4: 80%\n bucket 2: 80%\n bucket 4: 90%\n bucket 1: 100%\n bucket 2: 90%\n Sorting block of length 127 for bucket 1\n bucket 4: 100%\n (Using difference cover)\n bucket 2: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n bucket 3: 70%\n bucket 3: 80%\n bucket 3: 90%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 6:\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\n bucket 10: 40%\n bucket 9: 60%\n bucket 10: 50%\n bucket 9: 70%\n bucket 10: 60%\n bucket 10: 70%\n bucket 9: 80%\n bucket 10: 80%\n bucket 9: 90%\n bucket 10: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\nGetting block 12 of 29\n bucket 11: 60%\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 70%\n Entering block accumulator loop for bucket 12:\n bucket 11: 80%\n bucket 12: 10%\n bucket 11: 90%\n bucket 12: 20%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 16: 20%\n bucket 15: 40%\n bucket 16: 30%\n bucket 15: 50%\n bucket 16: 40%\n bucket 15: 60%\n bucket 16: 50%\n bucket 15: 70%\n bucket 16: 60%\n bucket 16: 70%\n bucket 15: 80%\n bucket 16: 80%\n bucket 15: 90%\n bucket 16: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n Sorting block time: 00:00:00\n bucket 20: 40%\nReturning block of 162 for bucket 19\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 26:\n bucket 25: 10%\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 25: 20%\n bucket 26: 40%\n bucket 25: 30%\n bucket 26: 50%\n bucket 26: 60%\n bucket 25: 40%\n bucket 26: 70%\n bucket 25: 50%\n bucket 26: 80%\n bucket 26: 90%\n bucket 25: 60%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n3 reads; of these:\n 3 (100.00%) were unpaired; of these:\n 3 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n3 reads; of these:\n 3 (100.00%) were unpaired; of these:\n 3 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\nGetting block 2 of 29\n Reserving size (252) for bucket 2\nGetting block 3 of 29\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n Reserving size (252) for bucket 3\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 3:\n bucket 1: 10%\n bucket 4: 10%\n bucket 2: 10%\n bucket 1: 20%\n bucket 4: 20%\n bucket 3: 10%\n bucket 2: 20%\n bucket 1: 30%\n bucket 4: 30%\n bucket 3: 20%\n bucket 2: 30%\n bucket 1: 40%\n bucket 4: 40%\n bucket 2: 40%\n bucket 1: 50%\n bucket 4: 50%\n bucket 2: 50%\n bucket 1: 60%\n bucket 3: 30%\n bucket 2: 60%\n bucket 1: 70%\n bucket 3: 40%\n bucket 4: 60%\n bucket 1: 80%\n bucket 2: 70%\n bucket 3: 50%\n bucket 4: 70%\n bucket 1: 90%\n bucket 3: 60%\n bucket 4: 80%\n bucket 2: 80%\n bucket 4: 90%\n bucket 1: 100%\n bucket 2: 90%\n Sorting block of length 127 for bucket 1\n bucket 4: 100%\n (Using difference cover)\n bucket 2: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n bucket 3: 70%\n bucket 3: 80%\n bucket 3: 90%\n bucket 3: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 6:\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\n bucket 7: 30%\n bucket 7: 40%\n bucket 7: 50%\n bucket 7: 60%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 8: 20%\n bucket 8: 30%\n bucket 8: 40%\n bucket 8: 50%\n bucket 8: 60%\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\n bucket 10: 40%\n bucket 9: 60%\n bucket 10: 50%\n bucket 9: 70%\n bucket 10: 60%\n bucket 10: 70%\n bucket 9: 80%\n bucket 10: 80%\n bucket 9: 90%\n bucket 10: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\nGetting block 12 of 29\n bucket 11: 60%\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 70%\n Entering block accumulator loop for bucket 12:\n bucket 11: 80%\n bucket 12: 10%\n bucket 11: 90%\n bucket 12: 20%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 16: 20%\n bucket 15: 40%\n bucket 16: 30%\n bucket 15: 50%\n bucket 16: 40%\n bucket 15: 60%\n bucket 16: 50%\n bucket 15: 70%\n bucket 16: 60%\n bucket 16: 70%\n bucket 15: 80%\n bucket 16: 80%\n bucket 15: 90%\n bucket 16: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n Sorting block time: 00:00:00\n bucket 20: 40%\nReturning block of 162 for bucket 19\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 26:\n bucket 25: 10%\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 25: 20%\n bucket 26: 40%\n bucket 25: 30%\n bucket 26: 50%\n bucket 26: 60%\n bucket 25: 40%\n bucket 26: 70%\n bucket 25: 50%\n bucket 26: 80%\n bucket 26: 90%\n bucket 25: 60%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "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": "2023-10-24 15:01:02", "plugin": "core", "name": "end_epoch", "raw_value": "1698159662.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:01:02", "plugin": "core", "name": "start_epoch", "raw_value": "1698159662.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-6", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 6, "time_seconds": 133.12181282043457, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "ada4ab0420946d18"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "6b508de4b8ff81b8"}, "library|input_2": {"src": "hda", "id": "6b508de4b8ff81b8"}, "library|type": "paired", "adv|output_options|unaligned_file": true, "adv|output_options|aligned_file": true, "adv|output_options|output_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "1ad10c8dbe64ac9d", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:03:24.542346", "create_time": "2023-10-24T15:01:23.833425", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-xk5n9", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/c/7/d/dataset_c7d5073b-f284-45d1-8af7-a7ae32604fa3.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/9/e/c/dataset_9eca0bdd-6605-4a80-b4ff-c8e934ec662e.dat' input_f.fasta && ln -f -s '/galaxy/server/database/objects/9/e/c/dataset_9eca0bdd-6605-4a80-b4ff-c8e934ec662e.dat' input_r.fasta && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -f -1 'input_f.fasta' -2 'input_r.fasta' --un-conc '/galaxy/server/database/objects/b/d/f/dataset_bdf41dae-25f8-4b10-9e31-6e5f67d1800a.dat' --al-conc '/galaxy/server/database/objects/7/5/1/dataset_7514c687-6d8d-48cf-8513-95b529fe13f5.dat' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/6/2/4/dataset_62475184-caa0-4025-8165-3f0879a73c86.dat' && mv '/galaxy/server/database/objects/b/d/f/dataset_bdf41dae-25f8-4b10-9e31-6e5f67d1800a.1.dat' '/galaxy/server/database/objects/b/d/f/dataset_bdf41dae-25f8-4b10-9e31-6e5f67d1800a.dat' && mv '/galaxy/server/database/objects/b/d/f/dataset_bdf41dae-25f8-4b10-9e31-6e5f67d1800a.2.dat' '/galaxy/server/database/objects/5/3/c/dataset_53c5001b-a1ff-4788-a24f-be4e257e577a.dat' && mv '/galaxy/server/database/objects/7/5/1/dataset_7514c687-6d8d-48cf-8513-95b529fe13f5.1.dat' '/galaxy/server/database/objects/7/5/1/dataset_7514c687-6d8d-48cf-8513-95b529fe13f5.dat' && mv '/galaxy/server/database/objects/7/5/1/dataset_7514c687-6d8d-48cf-8513-95b529fe13f5.2.dat' '/galaxy/server/database/objects/7/5/3/dataset_753d7628-a8d2-4e90-90e5-62ca08409cef.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 1, \"aligned_file\": \"true\", \"output_options_selector\": \"advanced\", \"unaligned_file\": \"true\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 201, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 201, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 200, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "ada4ab0420946d18", "src": "hda", "uuid": "c7d5073b-f284-45d1-8af7-a7ae32604fa3"}, "input_1": {"id": "6b508de4b8ff81b8", "src": "hda", "uuid": "9eca0bdd-6605-4a80-b4ff-c8e934ec662e"}, "input_2": {"id": "6b508de4b8ff81b8", "src": "hda", "uuid": "9eca0bdd-6605-4a80-b4ff-c8e934ec662e"}}, "outputs": {"output_alignments": {"id": "36abbaf006bc689e", "src": "hda", "uuid": "62475184-caa0-4025-8165-3f0879a73c86"}, "output_unaligned_reads_l": {"id": "0662bc0b5f5280ef", "src": "hda", "uuid": "bdf41dae-25f8-4b10-9e31-6e5f67d1800a"}, "output_aligned_reads_l": {"id": "e7529373321c101a", "src": "hda", "uuid": "7514c687-6d8d-48cf-8513-95b529fe13f5"}, "output_unaligned_reads_r": {"id": "6f5251d064e6c4ae", "src": "hda", "uuid": "53c5001b-a1ff-4788-a24f-be4e257e577a"}, "output_aligned_reads_r": {"id": "af7021138c19034b", "src": "hda", "uuid": "753d7628-a8d2-4e90-90e5-62ca08409cef"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\nGetting block 2 of 29\nGetting block 3 of 29\n Reserving size (252) for bucket 3\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n Calculating Z arrays for bucket 3\n Reserving size (252) for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 4:\n bucket 1: 10%\n Entering block accumulator loop for bucket 2:\n bucket 3: 10%\n bucket 4: 10%\n bucket 1: 20%\n bucket 2: 10%\n bucket 4: 20%\n bucket 1: 30%\n bucket 3: 20%\n bucket 4: 30%\n bucket 1: 40%\n bucket 3: 30%\n bucket 4: 40%\n bucket 1: 50%\n bucket 3: 40%\n bucket 4: 50%\n bucket 1: 60%\n bucket 3: 50%\n bucket 4: 60%\n bucket 2: 20%\n bucket 1: 70%\n bucket 3: 60%\n bucket 4: 70%\n bucket 2: 30%\n bucket 3: 70%\n bucket 4: 80%\n bucket 2: 40%\n bucket 1: 80%\n bucket 3: 80%\n bucket 2: 50%\n bucket 4: 90%\n bucket 1: 90%\n bucket 3: 90%\n bucket 2: 60%\n bucket 4: 100%\n bucket 3: 100%\n bucket 1: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 2: 70%\n Sorting block of length 127 for bucket 1\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n (Using difference cover)\n bucket 2: 80%\n bucket 2: 90%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n bucket 5: 70%\n Calculating Z arrays for bucket 6\n bucket 5: 80%\n bucket 5: 90%\n Entering block accumulator loop for bucket 6:\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 7:\n bucket 8: 10%\n bucket 7: 10%\n bucket 8: 20%\n bucket 7: 20%\n bucket 8: 30%\n bucket 7: 30%\n bucket 8: 40%\n bucket 7: 40%\n bucket 8: 50%\n bucket 7: 50%\n bucket 8: 60%\n bucket 7: 60%\n bucket 8: 70%\n bucket 7: 70%\n bucket 8: 80%\n bucket 7: 80%\n bucket 8: 90%\n bucket 7: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n bucket 11: 30%\n Calculating Z arrays for bucket 12\n bucket 11: 40%\n Entering block accumulator loop for bucket 12:\n bucket 11: 50%\n bucket 12: 10%\n bucket 11: 60%\n bucket 12: 20%\n bucket 11: 70%\n bucket 12: 30%\n bucket 11: 80%\n bucket 12: 40%\n bucket 11: 90%\n bucket 12: 50%\n bucket 11: 100%\n bucket 12: 60%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 13\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\n Entering block accumulator loop for bucket 14:\n bucket 13: 10%\n bucket 14: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 14: 20%\n bucket 13: 40%\n bucket 14: 30%\n bucket 13: 50%\n bucket 14: 40%\n bucket 13: 60%\n bucket 14: 50%\n bucket 13: 70%\n bucket 14: 60%\n bucket 13: 80%\n bucket 14: 70%\n bucket 13: 90%\n bucket 14: 80%\n bucket 13: 100%\n bucket 14: 90%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Entering block accumulator loop for bucket 20:\n Calculating Z arrays for bucket 21\n bucket 20: 10%\n Entering block accumulator loop for bucket 21:\n bucket 20: 20%\n bucket 21: 10%\n bucket 20: 30%\n bucket 21: 20%\n bucket 20: 40%\n bucket 21: 30%\n bucket 20: 50%\n bucket 21: 40%\n bucket 20: 60%\n bucket 21: 50%\n bucket 20: 70%\n bucket 21: 60%\n bucket 20: 80%\n bucket 21: 70%\n bucket 20: 90%\n bucket 21: 80%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 24: 10%\n bucket 23: 20%\n bucket 24: 20%\n bucket 23: 30%\n bucket 24: 30%\n bucket 23: 40%\n bucket 24: 40%\n bucket 23: 50%\n bucket 24: 50%\n bucket 23: 60%\n bucket 24: 60%\n bucket 23: 70%\n bucket 24: 70%\n bucket 23: 80%\n bucket 24: 80%\n bucket 23: 90%\n bucket 24: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 28: 10%\n bucket 27: 30%\n bucket 28: 20%\n bucket 27: 40%\n bucket 28: 30%\n bucket 27: 50%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 27: 60%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n3 reads; of these:\n 3 (100.00%) were paired; of these:\n 3 (100.00%) aligned concordantly 0 times\n 0 (0.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 6 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n3 reads; of these:\n 3 (100.00%) were paired; of these:\n 3 (100.00%) aligned concordantly 0 times\n 0 (0.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 6 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\nGetting block 2 of 29\nGetting block 3 of 29\n Reserving size (252) for bucket 3\nGetting block 4 of 29\n Reserving size (252) for bucket 4\n Calculating Z arrays for bucket 3\n Reserving size (252) for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 4:\n bucket 1: 10%\n Entering block accumulator loop for bucket 2:\n bucket 3: 10%\n bucket 4: 10%\n bucket 1: 20%\n bucket 2: 10%\n bucket 4: 20%\n bucket 1: 30%\n bucket 3: 20%\n bucket 4: 30%\n bucket 1: 40%\n bucket 3: 30%\n bucket 4: 40%\n bucket 1: 50%\n bucket 3: 40%\n bucket 4: 50%\n bucket 1: 60%\n bucket 3: 50%\n bucket 4: 60%\n bucket 2: 20%\n bucket 1: 70%\n bucket 3: 60%\n bucket 4: 70%\n bucket 2: 30%\n bucket 3: 70%\n bucket 4: 80%\n bucket 2: 40%\n bucket 1: 80%\n bucket 3: 80%\n bucket 2: 50%\n bucket 4: 90%\n bucket 1: 90%\n bucket 3: 90%\n bucket 2: 60%\n bucket 4: 100%\n bucket 3: 100%\n bucket 1: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 2: 70%\n Sorting block of length 127 for bucket 1\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n (Using difference cover)\n bucket 2: 80%\n bucket 2: 90%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n bucket 5: 70%\n Calculating Z arrays for bucket 6\n bucket 5: 80%\n bucket 5: 90%\n Entering block accumulator loop for bucket 6:\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 10%\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 7:\n bucket 8: 10%\n bucket 7: 10%\n bucket 8: 20%\n bucket 7: 20%\n bucket 8: 30%\n bucket 7: 30%\n bucket 8: 40%\n bucket 7: 40%\n bucket 8: 50%\n bucket 7: 50%\n bucket 8: 60%\n bucket 7: 60%\n bucket 8: 70%\n bucket 7: 70%\n bucket 8: 80%\n bucket 7: 80%\n bucket 8: 90%\n bucket 7: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n bucket 11: 30%\n Calculating Z arrays for bucket 12\n bucket 11: 40%\n Entering block accumulator loop for bucket 12:\n bucket 11: 50%\n bucket 12: 10%\n bucket 11: 60%\n bucket 12: 20%\n bucket 11: 70%\n bucket 12: 30%\n bucket 11: 80%\n bucket 12: 40%\n bucket 11: 90%\n bucket 12: 50%\n bucket 11: 100%\n bucket 12: 60%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 13\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\n Entering block accumulator loop for bucket 14:\n bucket 13: 10%\n bucket 14: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 14: 20%\n bucket 13: 40%\n bucket 14: 30%\n bucket 13: 50%\n bucket 14: 40%\n bucket 13: 60%\n bucket 14: 50%\n bucket 13: 70%\n bucket 14: 60%\n bucket 13: 80%\n bucket 14: 70%\n bucket 13: 90%\n bucket 14: 80%\n bucket 13: 100%\n bucket 14: 90%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Entering block accumulator loop for bucket 20:\n Calculating Z arrays for bucket 21\n bucket 20: 10%\n Entering block accumulator loop for bucket 21:\n bucket 20: 20%\n bucket 21: 10%\n bucket 20: 30%\n bucket 21: 20%\n bucket 20: 40%\n bucket 21: 30%\n bucket 20: 50%\n bucket 21: 40%\n bucket 20: 60%\n bucket 21: 50%\n bucket 20: 70%\n bucket 21: 60%\n bucket 20: 80%\n bucket 21: 70%\n bucket 20: 90%\n bucket 21: 80%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 24: 10%\n bucket 23: 20%\n bucket 24: 20%\n bucket 23: 30%\n bucket 24: 30%\n bucket 23: 40%\n bucket 24: 40%\n bucket 23: 50%\n bucket 24: 50%\n bucket 23: 60%\n bucket 24: 60%\n bucket 23: 70%\n bucket 24: 70%\n bucket 23: 80%\n bucket 24: 80%\n bucket 23: 90%\n bucket 24: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 28: 10%\n bucket 27: 30%\n bucket 28: 20%\n bucket 27: 40%\n bucket 28: 30%\n bucket 27: 50%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 27: 60%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\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": "2023-10-24 15:03:15", "plugin": "core", "name": "end_epoch", "raw_value": "1698159795.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:03:14", "plugin": "core", "name": "start_epoch", "raw_value": "1698159794.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-7", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 7, "time_seconds": 136.74872612953186, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "f27ecf990e1a1681"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "b517382fe49a404e"}, "library|input_2": {"src": "hda", "id": "eea49114f6871dd0"}, "library|paired_options|no_mixed": true, "library|paired_options|no_discordant": true, "library|paired_options|paired_options_selector": "advanced", "library|type": "paired", "adv|input_options|trim5": "15", "adv|input_options|trim3": "15", "adv|input_options|input_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "94619fc465ac7c18", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:05:41.547411", "create_time": "2023-10-24T15:03:40.577168", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-tx5hd", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/3/9/d/dataset_39d7c07c-c7f0-471f-ad7a-4dedb5a04f90.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/7/5/1/dataset_751ab1eb-3527-4423-bd49-6dd5535b44d4.dat' input_f.fastq.gz && ln -f -s '/galaxy/server/database/objects/c/d/2/dataset_cd278a86-462d-49b2-8927-63967087b3d3.dat' input_r.fastq.gz && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq.gz' -2 'input_r.fastq.gz' --fr --no-mixed --no-discordant --trim5 '15' --trim3 '15' --phred33 | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/6/5/5/dataset_6559e6f5-319d-4050-80fa-2054e7d4916c.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 1, \"input_options_selector\": \"advanced\", \"int_quals\": \"false\", \"qupto\": \"0\", \"qv_encoding\": \"--phred33\", \"skip\": \"0\", \"solexa_quals\": \"false\", \"trim3\": \"15\", \"trim5\": \"15\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 208, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 209, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"fr_rf_ff\": \"--fr\", \"no_discordant\": \"true\", \"no_mixed\": \"true\", \"paired_options_selector\": \"advanced\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 207, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "f27ecf990e1a1681", "src": "hda", "uuid": "39d7c07c-c7f0-471f-ad7a-4dedb5a04f90"}, "input_1": {"id": "b517382fe49a404e", "src": "hda", "uuid": "751ab1eb-3527-4423-bd49-6dd5535b44d4"}, "input_2": {"id": "eea49114f6871dd0", "src": "hda", "uuid": "cd278a86-462d-49b2-8927-63967087b3d3"}}, "outputs": {"output_alignments": {"id": "239db3f327077feb", "src": "hda", "uuid": "6559e6f5-319d-4050-80fa-2054e7d4916c"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\nGetting block 2 of 29\n Calculating Z arrays for bucket 1\n Reserving size (252) for bucket 2\nGetting block 4 of 29\nGetting block 3 of 29\n Reserving size (252) for bucket 4\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Reserving size (252) for bucket 3\n Calculating Z arrays for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 4:\n bucket 1: 20%\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n bucket 4: 10%\n Entering block accumulator loop for bucket 3:\n bucket 1: 40%\n bucket 2: 10%\n bucket 4: 20%\n bucket 1: 50%\n bucket 3: 10%\n bucket 2: 20%\n bucket 4: 30%\n bucket 1: 60%\n bucket 3: 20%\n bucket 2: 30%\n bucket 4: 40%\n bucket 1: 70%\n bucket 3: 30%\n bucket 2: 40%\n bucket 1: 80%\n bucket 3: 40%\n bucket 4: 50%\n bucket 1: 90%\n bucket 2: 50%\n bucket 3: 50%\n bucket 4: 60%\n bucket 1: 100%\n bucket 2: 60%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 3: 60%\n bucket 2: 70%\n bucket 4: 70%\n bucket 3: 70%\n bucket 2: 80%\n bucket 4: 80%\n bucket 3: 80%\n bucket 2: 90%\n bucket 4: 90%\n bucket 3: 90%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n bucket 4: 100%\n (Using difference cover)\n bucket 3: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n bucket 5: 30%\n Calculating Z arrays for bucket 6\n bucket 5: 40%\n bucket 5: 50%\n Entering block accumulator loop for bucket 6:\n bucket 5: 60%\n bucket 6: 10%\n bucket 5: 70%\n bucket 6: 20%\n bucket 5: 80%\n bucket 6: 30%\n bucket 5: 90%\n bucket 6: 40%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n bucket 7: 30%\n Calculating Z arrays for bucket 8\n bucket 7: 40%\n Entering block accumulator loop for bucket 8:\n bucket 7: 50%\n bucket 8: 10%\n bucket 7: 60%\n bucket 8: 20%\n bucket 7: 70%\n bucket 8: 30%\n bucket 7: 80%\n bucket 8: 40%\n bucket 7: 90%\n bucket 8: 50%\n bucket 8: 60%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n bucket 8: 70%\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\nGetting block 10 of 29\n Reserving size (252) for bucket 9\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 9\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 9: 50%\n bucket 10: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 10: 60%\n bucket 9: 80%\n bucket 10: 70%\n bucket 9: 90%\n bucket 10: 80%\n bucket 9: 100%\n bucket 10: 90%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 60%\n Entering block accumulator loop for bucket 12:\n bucket 11: 70%\n bucket 11: 80%\n bucket 12: 10%\n bucket 11: 90%\n bucket 12: 20%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\nGetting block 14 of 29\n Calculating Z arrays for bucket 13\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 13: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 13: 30%\n bucket 14: 50%\n bucket 13: 40%\n bucket 14: 60%\n bucket 13: 50%\n bucket 14: 70%\n bucket 13: 60%\n bucket 14: 80%\n bucket 13: 70%\n bucket 14: 90%\n bucket 13: 80%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 15 of 29\nGetting block 16 of 29\n Reserving size (252) for bucket 15\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 15\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 16: 10%\n bucket 15: 20%\n bucket 16: 20%\n bucket 15: 30%\n bucket 16: 30%\n bucket 15: 40%\n bucket 16: 40%\n bucket 15: 50%\n bucket 16: 50%\n bucket 15: 60%\n bucket 16: 60%\n bucket 15: 70%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block time: 00:00:00\n Sorting block of length 177 for bucket 15\n (Using difference cover)\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 20%\n bucket 17: 30%\n Entering block accumulator loop for bucket 18:\n bucket 17: 40%\n bucket 17: 50%\n bucket 18: 10%\n bucket 17: 60%\n bucket 18: 20%\n bucket 17: 70%\n bucket 18: 30%\n bucket 18: 40%\n bucket 17: 80%\n bucket 18: 50%\n bucket 17: 90%\n bucket 18: 60%\n bucket 17: 100%\n bucket 18: 70%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n bucket 20: 10%\n Calculating Z arrays for bucket 21\n bucket 20: 20%\n Entering block accumulator loop for bucket 21:\n bucket 20: 30%\n bucket 21: 10%\n bucket 20: 40%\n bucket 21: 20%\n bucket 20: 50%\n bucket 21: 30%\n bucket 20: 60%\n bucket 21: 40%\n bucket 20: 70%\n bucket 21: 50%\n bucket 20: 80%\n bucket 21: 60%\n bucket 20: 90%\n bucket 21: 70%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n bucket 22: 30%\n Calculating Z arrays for bucket 23\n bucket 22: 40%\n bucket 22: 50%\n Entering block accumulator loop for bucket 23:\n bucket 22: 60%\n bucket 23: 10%\n bucket 22: 70%\n bucket 23: 20%\n bucket 22: 80%\n bucket 23: 30%\n bucket 22: 90%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\nGetting block 27 of 29\n bucket 26: 80%\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\nGetting block 2 of 29\n Calculating Z arrays for bucket 1\n Reserving size (252) for bucket 2\nGetting block 4 of 29\nGetting block 3 of 29\n Reserving size (252) for bucket 4\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Reserving size (252) for bucket 3\n Calculating Z arrays for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 4:\n bucket 1: 20%\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n bucket 4: 10%\n Entering block accumulator loop for bucket 3:\n bucket 1: 40%\n bucket 2: 10%\n bucket 4: 20%\n bucket 1: 50%\n bucket 3: 10%\n bucket 2: 20%\n bucket 4: 30%\n bucket 1: 60%\n bucket 3: 20%\n bucket 2: 30%\n bucket 4: 40%\n bucket 1: 70%\n bucket 3: 30%\n bucket 2: 40%\n bucket 1: 80%\n bucket 3: 40%\n bucket 4: 50%\n bucket 1: 90%\n bucket 2: 50%\n bucket 3: 50%\n bucket 4: 60%\n bucket 1: 100%\n bucket 2: 60%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 3: 60%\n bucket 2: 70%\n bucket 4: 70%\n bucket 3: 70%\n bucket 2: 80%\n bucket 4: 80%\n bucket 3: 80%\n bucket 2: 90%\n bucket 4: 90%\n bucket 3: 90%\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n bucket 4: 100%\n (Using difference cover)\n bucket 3: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n bucket 5: 30%\n Calculating Z arrays for bucket 6\n bucket 5: 40%\n bucket 5: 50%\n Entering block accumulator loop for bucket 6:\n bucket 5: 60%\n bucket 6: 10%\n bucket 5: 70%\n bucket 6: 20%\n bucket 5: 80%\n bucket 6: 30%\n bucket 5: 90%\n bucket 6: 40%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\n bucket 7: 20%\nGetting block 8 of 29\n Reserving size (252) for bucket 8\n bucket 7: 30%\n Calculating Z arrays for bucket 8\n bucket 7: 40%\n Entering block accumulator loop for bucket 8:\n bucket 7: 50%\n bucket 8: 10%\n bucket 7: 60%\n bucket 8: 20%\n bucket 7: 70%\n bucket 8: 30%\n bucket 7: 80%\n bucket 8: 40%\n bucket 7: 90%\n bucket 8: 50%\n bucket 8: 60%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n bucket 8: 70%\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\nGetting block 10 of 29\n Reserving size (252) for bucket 9\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 9\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 9: 50%\n bucket 10: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 10: 60%\n bucket 9: 80%\n bucket 10: 70%\n bucket 9: 90%\n bucket 10: 80%\n bucket 9: 100%\n bucket 10: 90%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 60%\n Entering block accumulator loop for bucket 12:\n bucket 11: 70%\n bucket 11: 80%\n bucket 12: 10%\n bucket 11: 90%\n bucket 12: 20%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\nGetting block 14 of 29\n Calculating Z arrays for bucket 13\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 13: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 13: 30%\n bucket 14: 50%\n bucket 13: 40%\n bucket 14: 60%\n bucket 13: 50%\n bucket 14: 70%\n bucket 13: 60%\n bucket 14: 80%\n bucket 13: 70%\n bucket 14: 90%\n bucket 13: 80%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 15 of 29\nGetting block 16 of 29\n Reserving size (252) for bucket 15\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 15\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 16: 10%\n bucket 15: 20%\n bucket 16: 20%\n bucket 15: 30%\n bucket 16: 30%\n bucket 15: 40%\n bucket 16: 40%\n bucket 15: 50%\n bucket 16: 50%\n bucket 15: 60%\n bucket 16: 60%\n bucket 15: 70%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block time: 00:00:00\n Sorting block of length 177 for bucket 15\n (Using difference cover)\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 20%\n bucket 17: 30%\n Entering block accumulator loop for bucket 18:\n bucket 17: 40%\n bucket 17: 50%\n bucket 18: 10%\n bucket 17: 60%\n bucket 18: 20%\n bucket 17: 70%\n bucket 18: 30%\n bucket 18: 40%\n bucket 17: 80%\n bucket 18: 50%\n bucket 17: 90%\n bucket 18: 60%\n bucket 17: 100%\n bucket 18: 70%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n bucket 20: 10%\n Calculating Z arrays for bucket 21\n bucket 20: 20%\n Entering block accumulator loop for bucket 21:\n bucket 20: 30%\n bucket 21: 10%\n bucket 20: 40%\n bucket 21: 20%\n bucket 20: 50%\n bucket 21: 30%\n bucket 20: 60%\n bucket 21: 40%\n bucket 20: 70%\n bucket 21: 50%\n bucket 20: 80%\n bucket 21: 60%\n bucket 20: 90%\n bucket 21: 70%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n bucket 22: 30%\n Calculating Z arrays for bucket 23\n bucket 22: 40%\n bucket 22: 50%\n Entering block accumulator loop for bucket 23:\n bucket 22: 60%\n bucket 23: 10%\n bucket 22: 70%\n bucket 23: 20%\n bucket 22: 80%\n bucket 23: 30%\n bucket 22: 90%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\nGetting block 27 of 29\n bucket 26: 80%\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\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": "2023-10-24 15:05:32", "plugin": "core", "name": "end_epoch", "raw_value": "1698159932.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:05:31", "plugin": "core", "name": "start_epoch", "raw_value": "1698159931.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-8", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 8, "time_seconds": 138.44951248168945, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "a5d0f49e88a1ab13"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "2410f0558124564e"}, "library|input_2": {"src": "hda", "id": "e24ac96877557892"}, "library|paired_options|no_mixed": true, "library|paired_options|no_discordant": true, "library|paired_options|paired_options_selector": "advanced", "library|type": "paired", "adv|input_options|trim5": "15", "adv|input_options|trim3": "15", "adv|input_options|input_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "00e58e0d5093fb1c", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:07:59.984105", "create_time": "2023-10-24T15:05:58.586537", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-v6lpz", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/d/c/9/dataset_dc940b45-fc71-4327-8a7d-f6483d5b916e.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/6/d/8/dataset_6d8daa26-1017-4749-bc53-1d0cac101366.dat' input_f.fastq.bz2 && ln -f -s '/galaxy/server/database/objects/d/3/5/dataset_d359fd2d-3ef5-4e43-93d0-5b6183d7e1b1.dat' input_r.fastq.bz2 && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq.bz2' -2 'input_r.fastq.bz2' --fr --no-mixed --no-discordant --trim5 '15' --trim3 '15' --phred33 | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/f/2/b/dataset_f2b719ed-f13c-48ba-a054-f165e219d092.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 1, \"input_options_selector\": \"advanced\", \"int_quals\": \"false\", \"qupto\": \"0\", \"qv_encoding\": \"--phred33\", \"skip\": \"0\", \"solexa_quals\": \"false\", \"trim3\": \"15\", \"trim5\": \"15\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 212, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 213, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"fr_rf_ff\": \"--fr\", \"no_discordant\": \"true\", \"no_mixed\": \"true\", \"paired_options_selector\": \"advanced\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 211, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "a5d0f49e88a1ab13", "src": "hda", "uuid": "dc940b45-fc71-4327-8a7d-f6483d5b916e"}, "input_1": {"id": "2410f0558124564e", "src": "hda", "uuid": "6d8daa26-1017-4749-bc53-1d0cac101366"}, "input_2": {"id": "e24ac96877557892", "src": "hda", "uuid": "d359fd2d-3ef5-4e43-93d0-5b6183d7e1b1"}}, "outputs": {"output_alignments": {"id": "89fca57359639074", "src": "hda", "uuid": "f2b719ed-f13c-48ba-a054-f165e219d092"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\n Reserving size (252) for bucket 2\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 20%\n Calculating Z arrays for bucket 3\n bucket 1: 30%\n bucket 2: 10%\n bucket 1: 40%\n bucket 2: 20%\n bucket 1: 50%\n Entering block accumulator loop for bucket 3:\n bucket 2: 30%\n bucket 1: 60%\nGetting block 4 of 29\n bucket 2: 40%\n Reserving size (252) for bucket 4\n bucket 1: 70%\n Calculating Z arrays for bucket 4\n bucket 2: 50%\n bucket 1: 80%\n bucket 3: 10%\n bucket 2: 60%\n bucket 1: 90%\n Entering block accumulator loop for bucket 4:\n bucket 3: 20%\n bucket 2: 70%\n bucket 1: 100%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 3: 30%\n bucket 2: 80%\n bucket 4: 10%\n bucket 3: 40%\n bucket 2: 90%\n bucket 4: 20%\n bucket 3: 50%\n bucket 2: 100%\n bucket 4: 30%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n bucket 3: 60%\n bucket 4: 40%\n bucket 3: 70%\n bucket 4: 50%\n bucket 3: 80%\n bucket 4: 60%\n bucket 3: 90%\n bucket 4: 70%\n bucket 3: 100%\n bucket 4: 80%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 6:\n bucket 6: 10%\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\nGetting block 8 of 29\n bucket 7: 20%\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n bucket 7: 30%\n Entering block accumulator loop for bucket 8:\n bucket 7: 40%\n bucket 8: 10%\n bucket 7: 50%\n bucket 8: 20%\n bucket 7: 60%\n bucket 8: 30%\n bucket 7: 70%\n bucket 8: 40%\n bucket 8: 50%\n bucket 7: 80%\n bucket 8: 60%\n bucket 7: 90%\n bucket 8: 70%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 13\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 13:\n bucket 14: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 13: 20%\n bucket 14: 40%\n bucket 14: 50%\n bucket 13: 30%\n bucket 14: 60%\n bucket 14: 70%\n bucket 13: 40%\n bucket 14: 80%\n bucket 13: 50%\n bucket 14: 90%\n bucket 14: 100%\n bucket 13: 60%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 29\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 70%\n bucket 16: 80%\n Entering block accumulator loop for bucket 17:\n bucket 16: 90%\n bucket 17: 10%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n bucket 17: 20%\n (Using difference cover)\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\nGetting block 24 of 29\n bucket 23: 30%\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n Entering block accumulator loop for bucket 24:\n bucket 23: 70%\n bucket 23: 80%\n bucket 24: 10%\n bucket 23: 90%\n bucket 23: 100%\n bucket 24: 20%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 29\n Reserving size (252) for bucket 2\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\nGetting block 3 of 29\n Reserving size (252) for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 20%\n Calculating Z arrays for bucket 3\n bucket 1: 30%\n bucket 2: 10%\n bucket 1: 40%\n bucket 2: 20%\n bucket 1: 50%\n Entering block accumulator loop for bucket 3:\n bucket 2: 30%\n bucket 1: 60%\nGetting block 4 of 29\n bucket 2: 40%\n Reserving size (252) for bucket 4\n bucket 1: 70%\n Calculating Z arrays for bucket 4\n bucket 2: 50%\n bucket 1: 80%\n bucket 3: 10%\n bucket 2: 60%\n bucket 1: 90%\n Entering block accumulator loop for bucket 4:\n bucket 3: 20%\n bucket 2: 70%\n bucket 1: 100%\n Sorting block of length 127 for bucket 1\n (Using difference cover)\n bucket 3: 30%\n bucket 2: 80%\n bucket 4: 10%\n bucket 3: 40%\n bucket 2: 90%\n bucket 4: 20%\n bucket 3: 50%\n bucket 2: 100%\n bucket 4: 30%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n bucket 3: 60%\n bucket 4: 40%\n bucket 3: 70%\n bucket 4: 50%\n bucket 3: 80%\n bucket 4: 60%\n bucket 3: 90%\n bucket 4: 70%\n bucket 3: 100%\n bucket 4: 80%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 6:\n bucket 6: 10%\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n bucket 6: 20%\n bucket 6: 30%\n bucket 6: 40%\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 7:\n bucket 7: 10%\nGetting block 8 of 29\n bucket 7: 20%\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n bucket 7: 30%\n Entering block accumulator loop for bucket 8:\n bucket 7: 40%\n bucket 8: 10%\n bucket 7: 50%\n bucket 8: 20%\n bucket 7: 60%\n bucket 8: 30%\n bucket 7: 70%\n bucket 8: 40%\n bucket 8: 50%\n bucket 7: 80%\n bucket 8: 60%\n bucket 7: 90%\n bucket 8: 70%\n bucket 7: 100%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\nGetting block 13 of 29\n Reserving size (252) for bucket 13\nGetting block 14 of 29\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 13\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 13:\n bucket 14: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 13: 20%\n bucket 14: 40%\n bucket 14: 50%\n bucket 13: 30%\n bucket 14: 60%\n bucket 14: 70%\n bucket 13: 40%\n bucket 14: 80%\n bucket 13: 50%\n bucket 14: 90%\n bucket 14: 100%\n bucket 13: 60%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 29\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 70%\n bucket 16: 80%\n Entering block accumulator loop for bucket 17:\n bucket 16: 90%\n bucket 17: 10%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n bucket 17: 20%\n (Using difference cover)\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\nGetting block 24 of 29\n bucket 23: 30%\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n Entering block accumulator loop for bucket 24:\n bucket 23: 70%\n bucket 23: 80%\n bucket 24: 10%\n bucket 23: 90%\n bucket 23: 100%\n bucket 24: 20%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\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": "2023-10-24 15:07:50", "plugin": "core", "name": "end_epoch", "raw_value": "1698160070.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:07:49", "plugin": "core", "name": "start_epoch", "raw_value": "1698160069.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-9", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 9, "time_seconds": 135.1087257862091, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "f543c4953424cb3d"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "2044e070029ea705"}, "library|input_2": {"src": "hda", "id": "8ce305b0dc0cb1bd"}, "library|rna_strandness": "FR", "library|type": "paired"}, "job": {"model_class": "Job", "id": "91dfc61a1c007612", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T15:10:15.513332", "create_time": "2023-10-24T15:08:17.164613", "galaxy_version": "21.09", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-46dxz", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/b/b/8/dataset_bb8bb94f-1cbb-4dcc-a8dc-a62b502d386e.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/7/8/2/dataset_78298a5f-2b70-4120-a54a-83c426ab65e0.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/4/0/5/dataset_405ffe92-c3ab-4c29-9197-b9eeb734704b.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' --rna-strandness FR | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/0/1/5/dataset_0154687c-0a63-487d-996c-618a4598efc1.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": \"false\", \"summary_file\": \"false\"}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 216, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 217, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"FR\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 215, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"history_item": {"id": "f543c4953424cb3d", "src": "hda", "uuid": "bb8bb94f-1cbb-4dcc-a8dc-a62b502d386e"}, "input_1": {"id": "2044e070029ea705", "src": "hda", "uuid": "78298a5f-2b70-4120-a54a-83c426ab65e0"}, "input_2": {"id": "8ce305b0dc0cb1bd", "src": "hda", "uuid": "405ffe92-c3ab-4c29-9197-b9eeb734704b"}}, "outputs": {"output_alignments": {"id": "c0f7e9f7ed8f1f9f", "src": "hda", "uuid": "0154687c-0a63-487d-996c-618a4598efc1"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\nGetting block 3 of 29\nGetting block 2 of 29\n Reserving size (252) for bucket 3\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 3\n Reserving size (252) for bucket 2\n Calculating Z arrays for bucket 1\nGetting block 4 of 29\n Calculating Z arrays for bucket 2\n Reserving size (252) for bucket 4\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 2:\n bucket 3: 10%\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 4:\n bucket 2: 10%\n bucket 3: 20%\n bucket 1: 10%\n bucket 4: 10%\n bucket 2: 20%\n bucket 3: 30%\n bucket 4: 20%\n bucket 1: 20%\n bucket 2: 30%\n bucket 3: 40%\n bucket 1: 30%\n bucket 4: 30%\n bucket 3: 50%\n bucket 2: 40%\n bucket 1: 40%\n bucket 4: 40%\n bucket 3: 60%\n bucket 1: 50%\n bucket 4: 50%\n bucket 2: 50%\n bucket 3: 70%\n bucket 1: 60%\n bucket 4: 60%\n bucket 2: 60%\n bucket 1: 70%\n bucket 3: 80%\n bucket 4: 70%\n bucket 1: 80%\n bucket 2: 70%\n bucket 3: 90%\n bucket 4: 80%\n bucket 1: 90%\n bucket 2: 80%\n bucket 4: 90%\n bucket 3: 100%\n bucket 1: 100%\n bucket 2: 90%\n bucket 4: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n Sorting block of length 127 for bucket 1\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n (Using difference cover)\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\nReturning block of 243 for bucket 4\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\nGetting block 8 of 29\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 6:\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 7:\n bucket 6: 10%\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n bucket 6: 20%\n bucket 7: 10%\n Entering block accumulator loop for bucket 8:\n bucket 6: 30%\n bucket 7: 20%\n bucket 8: 10%\n bucket 7: 30%\n bucket 6: 40%\n bucket 8: 20%\n bucket 7: 40%\n bucket 6: 50%\n bucket 8: 30%\n bucket 7: 50%\n bucket 8: 40%\n bucket 6: 60%\n bucket 7: 60%\n bucket 8: 50%\n bucket 6: 70%\n bucket 7: 70%\n bucket 6: 80%\n bucket 8: 60%\n bucket 7: 80%\n bucket 6: 90%\n bucket 8: 70%\n bucket 7: 90%\n bucket 6: 100%\n bucket 8: 80%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n bucket 7: 100%\n bucket 8: 90%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 12:\n bucket 11: 10%\n bucket 12: 10%\n bucket 11: 20%\n bucket 12: 20%\n bucket 11: 30%\n bucket 12: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 12: 40%\n bucket 11: 60%\n bucket 12: 50%\n bucket 11: 70%\n bucket 12: 60%\n bucket 11: 80%\n bucket 12: 70%\n bucket 11: 90%\n bucket 12: 80%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\nGetting block 14 of 29\n bucket 13: 40%\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n Entering block accumulator loop for bucket 14:\n bucket 13: 90%\n bucket 14: 10%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n bucket 14: 20%\n bucket 14: 30%\n (Using difference cover)\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 16: 20%\n bucket 15: 40%\n bucket 16: 30%\n bucket 15: 50%\n bucket 16: 40%\n bucket 15: 60%\n bucket 16: 50%\n bucket 15: 70%\n bucket 16: 60%\n bucket 15: 80%\n bucket 16: 70%\n bucket 15: 90%\n bucket 16: 80%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 50%\n Entering block accumulator loop for bucket 22:\n bucket 21: 60%\n bucket 22: 10%\n bucket 21: 70%\n bucket 22: 20%\n bucket 21: 80%\n bucket 22: 30%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n Entering block accumulator loop for bucket 27:\n bucket 28: 60%\n bucket 28: 70%\n bucket 27: 10%\n bucket 28: 80%\n bucket 27: 20%\n bucket 28: 90%\n bucket 27: 30%\n bucket 28: 100%\n bucket 27: 40%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\n", "job_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stderr": "\nSettings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 252 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 252 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "stdout": "\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 44 sample suffixes\nGenerating random suffixes\nQSorting 44 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 44 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 20; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 2; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 1, merged 1; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 184.759 (target: 251)\nGetting block 1 of 29\nGetting block 3 of 29\nGetting block 2 of 29\n Reserving size (252) for bucket 3\n Reserving size (252) for bucket 1\n Calculating Z arrays for bucket 3\n Reserving size (252) for bucket 2\n Calculating Z arrays for bucket 1\nGetting block 4 of 29\n Calculating Z arrays for bucket 2\n Reserving size (252) for bucket 4\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 2:\n bucket 3: 10%\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 4:\n bucket 2: 10%\n bucket 3: 20%\n bucket 1: 10%\n bucket 4: 10%\n bucket 2: 20%\n bucket 3: 30%\n bucket 4: 20%\n bucket 1: 20%\n bucket 2: 30%\n bucket 3: 40%\n bucket 1: 30%\n bucket 4: 30%\n bucket 3: 50%\n bucket 2: 40%\n bucket 1: 40%\n bucket 4: 40%\n bucket 3: 60%\n bucket 1: 50%\n bucket 4: 50%\n bucket 2: 50%\n bucket 3: 70%\n bucket 1: 60%\n bucket 4: 60%\n bucket 2: 60%\n bucket 1: 70%\n bucket 3: 80%\n bucket 4: 70%\n bucket 1: 80%\n bucket 2: 70%\n bucket 3: 90%\n bucket 4: 80%\n bucket 1: 90%\n bucket 2: 80%\n bucket 4: 90%\n bucket 3: 100%\n bucket 1: 100%\n bucket 2: 90%\n bucket 4: 100%\n Sorting block of length 166 for bucket 3\n (Using difference cover)\n Sorting block of length 127 for bucket 1\n Sorting block of length 242 for bucket 4\n (Using difference cover)\n (Using difference cover)\n bucket 2: 100%\n Sorting block of length 239 for bucket 2\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 167 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 128 for bucket 1\n Sorting block time: 00:00:00\n Sorting block time: 00:00:00\nReturning block of 240 for bucket 2\nReturning block of 243 for bucket 4\nGetting block 5 of 29\n Reserving size (252) for bucket 5\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 5:\n bucket 5: 10%\n bucket 5: 20%\n bucket 5: 30%\n bucket 5: 40%\n bucket 5: 50%\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 162 for bucket 5\n (Using difference cover)\nGetting block 6 of 29\n Reserving size (252) for bucket 6\n Calculating Z arrays for bucket 6\nGetting block 7 of 29\n Reserving size (252) for bucket 7\nGetting block 8 of 29\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 6:\n Reserving size (252) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 7:\n bucket 6: 10%\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 5\n bucket 6: 20%\n bucket 7: 10%\n Entering block accumulator loop for bucket 8:\n bucket 6: 30%\n bucket 7: 20%\n bucket 8: 10%\n bucket 7: 30%\n bucket 6: 40%\n bucket 8: 20%\n bucket 7: 40%\n bucket 6: 50%\n bucket 8: 30%\n bucket 7: 50%\n bucket 8: 40%\n bucket 6: 60%\n bucket 7: 60%\n bucket 8: 50%\n bucket 6: 70%\n bucket 7: 70%\n bucket 6: 80%\n bucket 8: 60%\n bucket 7: 80%\n bucket 6: 90%\n bucket 8: 70%\n bucket 7: 90%\n bucket 6: 100%\n bucket 8: 80%\n Sorting block of length 164 for bucket 6\n (Using difference cover)\n bucket 7: 100%\n bucket 8: 90%\n Sorting block of length 220 for bucket 7\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 242 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 165 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 243 for bucket 8\nGetting block 9 of 29\n Reserving size (252) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 216 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 217 for bucket 9\nGetting block 10 of 29\n Reserving size (252) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 214 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 215 for bucket 10\nGetting block 11 of 29\n Reserving size (252) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 29\n Reserving size (252) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 12:\n bucket 11: 10%\n bucket 12: 10%\n bucket 11: 20%\n bucket 12: 20%\n bucket 11: 30%\n bucket 12: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 12: 40%\n bucket 11: 60%\n bucket 12: 50%\n bucket 11: 70%\n bucket 12: 60%\n bucket 11: 80%\n bucket 12: 70%\n bucket 11: 90%\n bucket 12: 80%\n bucket 11: 100%\n Sorting block of length 229 for bucket 11\n (Using difference cover)\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 195 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 230 for bucket 11\nGetting block 13 of 29\n Reserving size (252) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\nGetting block 14 of 29\n bucket 13: 40%\n Reserving size (252) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n Entering block accumulator loop for bucket 14:\n bucket 13: 90%\n bucket 14: 10%\n bucket 13: 100%\n Sorting block of length 197 for bucket 13\n bucket 14: 20%\n bucket 14: 30%\n (Using difference cover)\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 191 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 198 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 192 for bucket 14\nGetting block 15 of 29\n Reserving size (252) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 29\n Reserving size (252) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 16: 20%\n bucket 15: 40%\n bucket 16: 30%\n bucket 15: 50%\n bucket 16: 40%\n bucket 15: 60%\n bucket 16: 50%\n bucket 15: 70%\n bucket 16: 60%\n bucket 15: 80%\n bucket 16: 70%\n bucket 15: 90%\n bucket 16: 80%\n bucket 15: 100%\n Sorting block of length 177 for bucket 15\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 102 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 178 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 103 for bucket 16\nGetting block 17 of 29\n Reserving size (252) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\nGetting block 18 of 29\n Reserving size (252) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 100%\n Sorting block of length 162 for bucket 17\n (Using difference cover)\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n Sorting block time: 00:00:00\nReturning block of 163 for bucket 17\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 117 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 18\nGetting block 19 of 29\n Reserving size (252) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 161 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 162 for bucket 19\nGetting block 20 of 29\n Reserving size (252) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 232 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 233 for bucket 20\nGetting block 21 of 29\n Reserving size (252) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\nGetting block 22 of 29\n Reserving size (252) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 50%\n Entering block accumulator loop for bucket 22:\n bucket 21: 60%\n bucket 22: 10%\n bucket 21: 70%\n bucket 22: 20%\n bucket 21: 80%\n bucket 22: 30%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 131 for bucket 21\n (Using difference cover)\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 220 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 132 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 221 for bucket 22\nGetting block 23 of 29\n Reserving size (252) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 141 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 142 for bucket 23\nGetting block 24 of 29\n Reserving size (252) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 196 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 197 for bucket 24\nGetting block 25 of 29\n Reserving size (252) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 227 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 228 for bucket 25\nGetting block 26 of 29\n Reserving size (252) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 195 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 26\nGetting block 27 of 29\n Reserving size (252) for bucket 27\nGetting block 28 of 29\n Reserving size (252) for bucket 28\n Calculating Z arrays for bucket 28\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n Entering block accumulator loop for bucket 27:\n bucket 28: 60%\n bucket 28: 70%\n bucket 27: 10%\n bucket 28: 80%\n bucket 27: 20%\n bucket 28: 90%\n bucket 27: 30%\n bucket 28: 100%\n bucket 27: 40%\n Sorting block of length 80 for bucket 28\n (Using difference cover)\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 233 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 234 for bucket 27\nGetting block 29 of 29\n Reserving size (252) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 180 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 181 for bucket 29\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": "2023-10-24 15:10:05", "plugin": "core", "name": "end_epoch", "raw_value": "1698160205.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 15:10:04", "plugin": "core", "name": "start_epoch", "raw_value": "1698160204.0000000"}, {"title": "Memory Allocated (MB)", "value": "12000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "ivar_removereads/1.2.2+galaxy1-0", "has_data": true, "data": {"tool_id": "ivar_removereads", "tool_version": "1.2.2+galaxy1", "test_index": 0, "time_seconds": 156.7400324344635, "inputs": {"input_bam": {"src": "hda", "id": "6d7bcfd887625969"}, "variants_tsv": {"src": "hda", "id": "79f0c54e21ce9037"}, "input_bed": {"src": "hda", "id": "33c7311fd0862619"}, "amplicon_info": {"src": "hda", "id": "9e30ea150f3170e6"}}, "job": {"model_class": "Job", "id": "ecd3a10224753a8c", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:46:58.397169", "create_time": "2023-10-24T14:44:44.945309", "galaxy_version": "21.09", "command_version": "iVar version 1.2.2", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1", "history_id": "639c57257ba4f009", "external_id": "gxy-wzn5p", "command_line": "cp '/galaxy/server/database/objects/1/1/0/dataset_110a263a-caa9-44ef-847a-6f7c971fff17.dat' binding_sites.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ee2beb764a7b/ivar_removereads/sanitize_bed.py' binding_sites.bed && ivar getmasked -i '/galaxy/server/database/objects/7/5/2/dataset_75287219-bb49-4e14-b5ce-be7df64d69a3.dat' -b binding_sites.bed -f '/galaxy/server/database/objects/e/f/8/dataset_ef8f9e43-f1be-4722-bc77-2db60b00e4ab.dat' -p masked_primers && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ee2beb764a7b/ivar_removereads/completemask.py' masked_primers.txt '/galaxy/server/database/objects/e/f/8/dataset_ef8f9e43-f1be-4722-bc77-2db60b00e4ab.dat' && ln -s '/galaxy/server/database/objects/c/3/c/dataset_c3c02551-2103-4395-9267-01de26996cc7.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/c/4/3/metadata_c4355deb-9acb-4211-b152-8353c288f82a.dat' sorted.bam.bai && ivar removereads -i sorted.bam -b binding_sites.bed -p removed_reads.bam -t masked_primers.txt", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input_bam": {"id": "6d7bcfd887625969", "src": "hda", "uuid": "c3c02551-2103-4395-9267-01de26996cc7"}, "variants_tsv": {"id": "79f0c54e21ce9037", "src": "hda", "uuid": "75287219-bb49-4e14-b5ce-be7df64d69a3"}, "input_bed": {"id": "33c7311fd0862619", "src": "hda", "uuid": "110a263a-caa9-44ef-847a-6f7c971fff17"}, "amplicon_info": {"id": "9e30ea150f3170e6", "src": "hda", "uuid": "ef8f9e43-f1be-4722-bc77-2db60b00e4ab"}}, "outputs": {"output_bam": {"id": "cda6e1d184ef4197", "src": "hda", "uuid": "cc583ea1-240d-4bc3-9651-5e67132abb27"}}, "output_collections": {}, "tool_stdout": "Found 67 primers in BED file\nPrimer pair for 400_1_out_R not found in BED file.\nPrimer pair for 400_34_out_L* not found in BED file.\nPrimer pair for 400_35_out_L not found in BED file.\n400_18_out_L**\t400_23_out_R\t400_32_out_L\n\nRemoving reads primed with any of:\n400_18_out_L**\t400_18_out_R**\t400_23_out_L\t400_23_out_R\t400_32_out_L\t400_32_out_R\nFound 67 primers in BED file\nWriting to removed_reads.bam\nNumber of references: 1\nReference Name: PRV\nReference Length: 10807\nUsing Region: PRV\nSorted By Coordinate\nResults:\n1629 reads were removed.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Found 67 primers in BED file\nPrimer pair for 400_1_out_R not found in BED file.\nPrimer pair for 400_34_out_L* not found in BED file.\nPrimer pair for 400_35_out_L not found in BED file.\n400_18_out_L**\t400_23_out_R\t400_32_out_L\n\nRemoving reads primed with any of:\n400_18_out_L**\t400_18_out_R**\t400_23_out_L\t400_23_out_R\t400_32_out_L\t400_32_out_R\nFound 67 primers in BED file\nWriting to removed_reads.bam\nNumber of references: 1\nReference Name: PRV\nReference Length: 10807\nUsing Region: PRV\nSorted By Coordinate\nResults:\n1629 reads were removed.\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": "2023-10-24 14:46:47", "plugin": "core", "name": "end_epoch", "raw_value": "1698158807.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:46:46", "plugin": "core", "name": "start_epoch", "raw_value": "1698158806.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "poretools_tabular/0.6.1a1.0-0", "has_data": true, "data": {"tool_id": "poretools_tabular", "tool_version": "0.6.1a1.0", "test_index": 0, "time_seconds": 165.48031544685364, "inputs": {"input": {"src": "hda", "id": "ca76b529ff0d5284"}}, "job": {"model_class": "Job", "id": "af2a5443882dbdd1", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:18:41.526934", "create_time": "2023-10-24T14:16:07.529576", "galaxy_version": "21.09", 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"params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "type": "\"all\""}, "inputs": {"input": {"id": "c67cb6056660516f", "src": "hda", "uuid": "f7bffaca-068e-4fa4-a4c4-7813c435d3d6"}}, "outputs": {"output": {"id": "2fb07bd5d6935c53", "src": "hda", "uuid": "9a6581f7-57b0-470d-b8f4-b91a678930a5"}}, "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": "2023-10-24 14:27:33", "plugin": "core", "name": "end_epoch", "raw_value": "1698157653.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:27:32", "plugin": "core", "name": "start_epoch", "raw_value": "1698157652.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_idxstats/2.0.4-0", "has_data": true, "data": {"tool_id": "samtools_idxstats", "tool_version": "2.0.4", "test_index": 0, "time_seconds": 136.36167669296265, "inputs": {"input": {"src": "hda", "id": "3579d0490385ce77"}}, "job": {"model_class": "Job", "id": "36669d7f8bd179b8", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:44:07.093021", "create_time": "2023-10-24T13:42:02.152411", "galaxy_version": "21.09", "command_version": "Version: 1.13 (using htslib 1.13)", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4", "history_id": "639c57257ba4f009", "external_id": "gxy-v2psm", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s 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{"__new_primary_file_list_output_tab|foo3.tab__": {"id": "d307f376c9f5099d", "src": "hda", "uuid": "c9920b1f-d01e-44bb-b22f-42bb6a9d5877"}, "__new_primary_file_list_output_tab|foo2.tab__": {"id": "78e6f5152b1d49ec", "src": "hda", "uuid": "51f3d30b-eeee-4ade-bb9b-f3d074c40fc2"}, "__new_primary_file_list_output_tab|foo.tab__": {"id": "3bcf1f44dbfa8587", "src": "hda", "uuid": "1ba92372-b391-4b9d-8a83-7a471c0a6319"}}, "output_collections": {"list_output_tab": {"id": "639c57257ba4f009", "src": "hdca"}}, "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": "2023-10-24 12:47:49", "plugin": "core", "name": "end_epoch", "raw_value": "1698151669.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 12:47:49", "plugin": "core", "name": "start_epoch", "raw_value": "1698151669.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-1", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 1, "time_seconds": 125.89348769187927, "inputs": {"split_parms|input": {"src": "hda", "id": "95eaf33b84196d13"}, "split_parms|top": "2", "split_parms|split_by|select_mode|numnew": "2", "split_parms|split_by|select_mode|mode": "numnew", "split_parms|split_by|newfilenames": "test", "split_parms|split_by|select_split_by": "row", "split_parms|select_ftype": "tabular"}, "job": {"model_class": "Job", "id": "d307f376c9f5099d", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T12:50:01.851826", "create_time": "2023-10-24T12:48:06.782922", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-8rhhq", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/9/3/5/dataset_93597112-144d-4a09-b4a8-378d5aa7f018.dat' --ftype 'tabular' --top '2' --by 'row' --numnew '2' --file_names 'test' --file_ext 'tabular'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 5, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 1, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"select_split_by\": \"row\"}, \"top\": \"2\"}"}, "inputs": {"input": {"id": "95eaf33b84196d13", "src": "hda", "uuid": "93597112-144d-4a09-b4a8-378d5aa7f018"}}, "outputs": {"__new_primary_file_list_output_tab|test_000001.tabular__": {"id": "1061adec31e025b4", "src": "hda", "uuid": "1ab15332-0c50-40b5-97ae-1a6a861365b3"}, "__new_primary_file_list_output_tab|test_000000.tabular__": {"id": "bc11060a229d1ae8", "src": "hda", "uuid": "b6aadf4b-9064-4a74-b478-7ed79d89c692"}}, "output_collections": {"list_output_tab": {"id": "3bcf1f44dbfa8587", "src": "hdca"}}, "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": "2023-10-24 12:49:57", "plugin": "core", "name": "end_epoch", "raw_value": "1698151797.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 12:49:57", "plugin": "core", "name": "start_epoch", "raw_value": "1698151797.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-10", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 10, "time_seconds": 124.1493079662323, "inputs": {"split_parms|input": {"src": "hda", "id": "bb3dfe72361b3c84"}, "split_parms|split_method|record_length": "4", "split_parms|split_method|select_split_method": "number", "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "test", "split_parms|select_ftype": "generic"}, "job": {"model_class": "Job", "id": "05afb11be5b57bdb", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:09:19.875165", "create_time": "2023-10-24T13:07:26.482147", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-g5b5k", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/2/9/f/dataset_29fbf238-717d-4659-b07f-a25daeaa0daa.dat' --ftype 'generic' --generic_num 4 --numnew '2' --file_names 'test' --file_ext 'fastq'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 6, \"input\": {\"values\": [{\"id\": 57, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"generic\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"split_method\": {\"__current_case__\": 1, \"record_length\": \"4\", \"select_split_method\": \"number\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input": {"id": "bb3dfe72361b3c84", "src": "hda", "uuid": "29fbf238-717d-4659-b07f-a25daeaa0daa"}}, "outputs": {"__new_primary_file_list_output_generic|test_000000__": {"id": "5d5b0f6cf0338406", "src": "hda", "uuid": "50b6bd07-8668-4e22-8d06-6de0d46ec4d5"}, "__new_primary_file_list_output_generic|test_000001__": {"id": "4f22e28d648b2f46", "src": "hda", "uuid": "33881e3b-8878-4373-af69-89eefef8dd23"}}, "output_collections": {"list_output_generic": {"id": "41998eb1e7c376e1", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:09:15", "plugin": "core", "name": "start_epoch", "raw_value": "1698152955.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:09:15", "plugin": "core", "name": "end_epoch", "raw_value": "1698152955.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-11", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 11, "time_seconds": 131.11482524871826, "inputs": {"split_parms|input": {"src": "hda", "id": "35facf84ffa5cb2c"}, "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "rand", "split_parms|select_allocate|seed": "1010", "split_parms|select_allocate|allocate": "random", "split_parms|select_ftype": "fasta"}, "job": {"model_class": "Job", "id": "5dc7a9949ffeb878", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:11:31.216440", "create_time": "2023-10-24T13:09:31.060215", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-gjx4l", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/8/a/d/dataset_8ad80633-98db-40ab-ab67-7c935f5f844d.dat' --ftype 'fasta' --numnew '2' --rand --seed '1010' --file_names 'rand' --file_ext 'fasta'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 3, \"input\": {\"values\": [{\"id\": 60, \"src\": \"hda\"}]}, \"newfilenames\": \"rand\", \"select_allocate\": {\"__current_case__\": 0, \"allocate\": \"random\", \"seed\": \"1010\"}, \"select_ftype\": \"fasta\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"input": {"id": "35facf84ffa5cb2c", "src": "hda", "uuid": "8ad80633-98db-40ab-ab67-7c935f5f844d"}}, "outputs": {"__new_primary_file_list_output_fasta|rand_000000.fasta__": {"id": "cd0497337d4aed6f", "src": "hda", "uuid": "d464b66a-6b0c-4669-a96d-2bbf88632413"}, "__new_primary_file_list_output_fasta|rand_000001.fasta__": {"id": "6bd4eb180716bded", "src": "hda", "uuid": "27a62ed0-8ede-4e7d-9cfd-750bdd603c35"}}, "output_collections": {"list_output_fasta": {"id": "8b45f74579ecd00b", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:11:26", "plugin": "core", "name": "start_epoch", "raw_value": "1698153086.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:11:26", "plugin": "core", "name": "end_epoch", "raw_value": "1698153086.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-12", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 12, "time_seconds": 122.23758316040039, "inputs": {"split_parms|input": {"src": "hda", "id": "d7736db3ad1919bf"}, "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "fasta_batch", "split_parms|select_allocate|allocate": "batch", "split_parms|select_ftype": "fasta"}, "job": {"model_class": "Job", "id": "3fb46099ab1f2343", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:13:33.567175", "create_time": "2023-10-24T13:11:41.586621", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-jgmgx", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/4/7/2/dataset_4720c506-6385-40d9-b4b0-d73b58c4d539.dat' --ftype 'fasta' --numnew '2' --batch --file_names 'fasta_batch' --file_ext 'fasta'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 3, \"input\": {\"values\": [{\"id\": 63, \"src\": \"hda\"}]}, \"newfilenames\": \"fasta_batch\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_ftype\": \"fasta\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"input": {"id": "d7736db3ad1919bf", "src": "hda", "uuid": "4720c506-6385-40d9-b4b0-d73b58c4d539"}}, "outputs": {"__new_primary_file_list_output_fasta|fasta_batch_000000.fasta__": {"id": "7f3623de2b97df5b", "src": "hda", "uuid": "fa267c49-9204-44cc-8adf-d62a14f4032e"}, "__new_primary_file_list_output_fasta|fasta_batch_000001.fasta__": {"id": "d18b1d153041ab26", "src": "hda", "uuid": "be040ab1-ab79-4c47-a564-404cdb826ff0"}}, "output_collections": {"list_output_fasta": {"id": "1408f9de6d7feaa3", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:13:28", "plugin": "core", "name": "start_epoch", "raw_value": "1698153208.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:13:28", "plugin": "core", "name": "end_epoch", "raw_value": "1698153208.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-13", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 13, "time_seconds": 125.4635841846466, "inputs": {"split_parms|input": {"src": "hda", "id": "81f3563e1a080f80"}, "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "test", "split_parms|select_ftype": "txt"}, "job": {"model_class": "Job", "id": "798564e7ae325875", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:15:38.973707", "create_time": "2023-10-24T13:13:43.893849", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-qjx2x", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/d/8/c/dataset_d8ca6d04-2a7b-4080-a1da-e6ee2c08267e.dat' --ftype 'txt' --numnew '2' --file_names 'test' --file_ext 'txt'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 5, \"input\": {\"values\": [{\"id\": 66, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"txt\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"txt\""}, "inputs": {"input": {"id": "81f3563e1a080f80", "src": "hda", "uuid": "d8ca6d04-2a7b-4080-a1da-e6ee2c08267e"}}, "outputs": {"__new_primary_file_list_output_txt|test_000000.txt__": {"id": "b9b004b9c1edd0cc", "src": "hda", "uuid": "1b3df26b-4274-4d6e-b44a-4642e141c708"}, "__new_primary_file_list_output_txt|test_000001.txt__": {"id": "5ae9b4b1aa3dde57", "src": "hda", "uuid": "82f9026e-67c9-4520-b25f-bd9505ccbf68"}}, "output_collections": {"list_output_txt": {"id": "d6529d98fa4d20e4", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:15:34", "plugin": "core", "name": "start_epoch", "raw_value": "1698153334.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:15:34", "plugin": "core", "name": "end_epoch", "raw_value": "1698153334.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-14", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 14, "time_seconds": 124.21081161499023, "inputs": {"split_parms|input": {"src": "hda", "id": "4c2d4cab830cc4ca"}, "split_parms|split_method|generic_regex": "^.*", "split_parms|split_method|select_split_method": "regex", "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "test", "split_parms|select_ftype": "generic"}, "job": {"model_class": "Job", "id": "e4210ace140f89c6", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:17:43.361538", "create_time": "2023-10-24T13:15:49.494207", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-w2jvs", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/9/0/a/dataset_90a822c5-02e8-4c62-b212-fbaf925c59f5.dat' --ftype 'generic' --generic_re '^.*' --numnew '2' --file_names 'test' --file_ext 'txt'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 6, \"input\": {\"values\": [{\"id\": 69, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"generic\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"split_method\": {\"__current_case__\": 0, \"generic_regex\": \"^.*\", \"select_split_method\": \"regex\", \"split_after\": \"false\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"txt\""}, "inputs": {"input": {"id": "4c2d4cab830cc4ca", "src": "hda", "uuid": "90a822c5-02e8-4c62-b212-fbaf925c59f5"}}, "outputs": {"__new_primary_file_list_output_generic|test_000000__": {"id": "72e076ef074a47a3", "src": "hda", "uuid": "19faec0d-7d90-41a9-a39c-3349c7d4a7fc"}, "__new_primary_file_list_output_generic|test_000001__": {"id": "0618f1b82d0862c7", "src": "hda", "uuid": "c35a491c-2f25-4649-b1e2-e0bfbbeb1d83"}}, "output_collections": {"list_output_generic": {"id": "90cb9477be57fb80", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:17:38", "plugin": "core", "name": "start_epoch", "raw_value": "1698153458.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:17:38", "plugin": "core", "name": "end_epoch", "raw_value": "1698153458.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-15", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 15, "time_seconds": 129.21465253829956, "inputs": {"split_parms|input": {"src": "hda", "id": "db0a006c0fc0c413"}, "split_parms|split_method|generic_regex": "^>.*", "split_parms|split_method|select_split_method": "regex", "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "rand", "split_parms|select_allocate|seed": "1010", "split_parms|select_allocate|allocate": "random", "split_parms|select_ftype": "generic"}, "job": {"model_class": "Job", "id": "733e4defa23258f2", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:19:52.794973", "create_time": "2023-10-24T13:17:53.781355", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-gzbhb", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/9/7/c/dataset_97cf0931-98d7-4a46-9a21-650bafaed439.dat' --ftype 'generic' --generic_re '^>.*' --numnew '2' --rand --seed '1010' --file_names 'rand' --file_ext 'fasta'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 6, \"input\": {\"values\": [{\"id\": 72, \"src\": \"hda\"}]}, \"newfilenames\": \"rand\", \"select_allocate\": {\"__current_case__\": 0, \"allocate\": \"random\", \"seed\": \"1010\"}, \"select_ftype\": \"generic\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"split_method\": {\"__current_case__\": 0, \"generic_regex\": \"^>.*\", \"select_split_method\": \"regex\", \"split_after\": \"false\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"input": {"id": "db0a006c0fc0c413", "src": "hda", "uuid": "97cf0931-98d7-4a46-9a21-650bafaed439"}}, "outputs": {"__new_primary_file_list_output_generic|rand_000000__": {"id": "6e2ae9a34bcdfeca", "src": "hda", "uuid": "badddc16-e8b6-4baf-9009-cda0ecbd8d22"}, "__new_primary_file_list_output_generic|rand_000001__": {"id": "fb065f9e39b7e79b", "src": "hda", "uuid": "bc1760e7-9146-4a6c-b4df-93b1ff6622f5"}}, "output_collections": {"list_output_generic": {"id": "dcad3eccc186af55", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:19:47", "plugin": "core", "name": "start_epoch", "raw_value": "1698153587.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:19:47", "plugin": "core", "name": "end_epoch", "raw_value": "1698153587.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-16", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 16, "time_seconds": 124.71707701683044, "inputs": {"split_parms|input": {"src": "hda", "id": "946a1dc799807f12"}, "split_parms|select_mode|numnew": "10", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "mol", "split_parms|select_allocate|allocate": "batch", "split_parms|select_ftype": "sdf"}, "job": {"model_class": "Job", "id": "61c23418ca407c16", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:21:57.175574", "create_time": "2023-10-24T13:20:03.830351", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-pqf8c", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/a/5/b/dataset_a5b9c92b-a8bb-492a-aad2-ee866000a9b9.dat' --ftype 'sdf' --numnew '10' --batch --file_names 'mol' --file_ext 'sdf'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 4, \"input\": {\"values\": [{\"id\": 75, \"src\": \"hda\"}]}, \"newfilenames\": \"mol\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_ftype\": \"sdf\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"10\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"sdf\""}, "inputs": {"input": {"id": "946a1dc799807f12", "src": "hda", "uuid": "a5b9c92b-a8bb-492a-aad2-ee866000a9b9"}}, "outputs": {"__new_primary_file_list_output_sdf|mol_000000.sdf__": {"id": "b4cb4228a1d2062b", "src": "hda", "uuid": "de1d69e5-4dff-47e2-a85e-4ef6e0de7060"}, "__new_primary_file_list_output_sdf|mol_000001.sdf__": {"id": "9419f18830f061c5", "src": "hda", "uuid": "42057a09-1b5f-4f75-8f75-a5cb0bdd6a78"}, "__new_primary_file_list_output_sdf|mol_000002.sdf__": {"id": "54e969cd1cecc0e7", "src": "hda", "uuid": "ac38840d-171b-4b13-941a-1f8ad2ae8fea"}}, "output_collections": {"list_output_sdf": {"id": "93fcde8a61d133d1", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:21:53", "plugin": "core", "name": "start_epoch", "raw_value": "1698153713.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:21:53", "plugin": "core", "name": "end_epoch", "raw_value": "1698153713.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-17", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 17, "time_seconds": 129.45859956741333, "inputs": {"split_parms|input": {"src": "hda", "id": "5963a56040137473"}, "split_parms|select_mode|chunksize": "1", "split_parms|select_mode|mode": "chunk", "split_parms|newfilenames": "mol", "split_parms|select_allocate|allocate": "batch", "split_parms|select_ftype": "sdf"}, "job": {"model_class": "Job", "id": "99b46ab0c011e874", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:24:06.522543", "create_time": "2023-10-24T13:22:08.220107", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-rb5mz", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/5/e/d/dataset_5edca437-db74-49b4-9769-f1f0c72081bc.dat' --ftype 'sdf' --chunksize 1 --batch --file_names 'mol' --file_ext 'sdf'", "traceback": null, "params": {"__input_ext": "\"sdf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 4, \"input\": {\"values\": [{\"id\": 79, \"src\": \"hda\"}]}, \"newfilenames\": \"mol\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_ftype\": \"sdf\", \"select_mode\": {\"__current_case__\": 0, \"chunksize\": \"1\", \"mode\": \"chunk\"}}"}, "inputs": {"input": {"id": "5963a56040137473", "src": "hda", "uuid": "5edca437-db74-49b4-9769-f1f0c72081bc"}}, "outputs": {"__new_primary_file_list_output_sdf|mol_000000.sdf__": {"id": "71a8d024bd56e8a0", "src": "hda", "uuid": "48ceab1d-4c74-4a5b-8f5b-8e06ed08953e"}, "__new_primary_file_list_output_sdf|mol_000001.sdf__": {"id": "2954a6385e78c99b", "src": "hda", "uuid": "d7401176-8121-452f-8ff8-8d87eb842c64"}, "__new_primary_file_list_output_sdf|mol_000002.sdf__": {"id": "af2a5443882dbdd1", "src": "hda", "uuid": "246df9ff-101e-48cd-9370-cea73b211af2"}}, "output_collections": {"list_output_sdf": {"id": "3671510065811f7e", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:24:01", "plugin": "core", "name": "start_epoch", "raw_value": "1698153841.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:24:01", "plugin": "core", "name": "end_epoch", "raw_value": "1698153841.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-18", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 18, "time_seconds": 128.61241555213928, "inputs": {"split_parms|input": {"src": "hda", "id": "da8e2a550c2efe17"}, "split_parms|split_method|generic_regex": "^[^>].*", "split_parms|split_method|split_after": "true", "split_parms|split_method|select_split_method": "regex", "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "rand", "split_parms|select_allocate|seed": "1010", "split_parms|select_allocate|allocate": "random", "split_parms|select_ftype": "generic"}, "job": {"model_class": "Job", "id": "ec35bec72ddbe584", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:26:15.826165", "create_time": "2023-10-24T13:24:17.472796", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-xhp8x", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/2/e/1/dataset_2e178a6a-4fb4-40a3-a918-80d39cd9d46f.dat' --ftype 'generic' --generic_re '^[^>].*' --split_after --numnew '2' --rand --seed '1010' --file_names 'rand' --file_ext 'fasta'", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 6, \"input\": {\"values\": [{\"id\": 83, \"src\": \"hda\"}]}, \"newfilenames\": \"rand\", \"select_allocate\": {\"__current_case__\": 0, \"allocate\": \"random\", \"seed\": \"1010\"}, \"select_ftype\": \"generic\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"split_method\": {\"__current_case__\": 0, \"generic_regex\": \"^[^>].*\", \"select_split_method\": \"regex\", \"split_after\": \"true\"}}"}, "inputs": {"input": {"id": "da8e2a550c2efe17", "src": "hda", "uuid": "2e178a6a-4fb4-40a3-a918-80d39cd9d46f"}}, "outputs": {"__new_primary_file_list_output_generic|rand_000000__": {"id": "9bda6edfe33d1744", "src": "hda", "uuid": "e22292fa-f9b1-442e-bc89-6b402ea6eeba"}, "__new_primary_file_list_output_generic|rand_000001__": {"id": "04365304d4f1bb57", "src": "hda", "uuid": "353a8f0b-889c-47aa-85ad-6f7b6cba0b40"}}, "output_collections": {"list_output_generic": {"id": "0c052697fe8e380d", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:26:11", "plugin": "core", "name": "start_epoch", "raw_value": "1698153971.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:26:11", "plugin": "core", "name": "end_epoch", "raw_value": "1698153971.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-2", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 2, "time_seconds": 127.11034607887268, "inputs": {"split_parms|input": {"src": "hda", "id": "6f1a7ccdcdcc2759"}, "split_parms|top": "2", "split_parms|split_by|select_mode|numnew": "2", "split_parms|split_by|select_mode|mode": "numnew", "split_parms|split_by|newfilenames": "batch_tab", "split_parms|split_by|select_allocate|allocate": "batch", "split_parms|split_by|select_split_by": "row", "split_parms|select_ftype": "tabular"}, "job": {"model_class": "Job", "id": "bc11060a229d1ae8", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T12:52:09.156893", "create_time": "2023-10-24T12:50:13.108180", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-8qhdz", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/2/3/a/dataset_23a4ceea-c2d3-4ff8-9527-3b060563e3bd.dat' --ftype 'tabular' --top '2' --by 'row' --numnew '2' --batch --file_names 'batch_tab' --file_ext 'tabular'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 8, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 1, \"newfilenames\": \"batch_tab\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}, \"select_split_by\": \"row\"}, \"top\": \"2\"}"}, "inputs": {"input": {"id": "6f1a7ccdcdcc2759", "src": "hda", "uuid": "23a4ceea-c2d3-4ff8-9527-3b060563e3bd"}}, "outputs": {"__new_primary_file_list_output_tab|batch_tab_000001.tabular__": {"id": "5e9469789eeb70d1", "src": "hda", "uuid": "354add99-79d5-43f9-9e5a-d0ad2f5a3e2f"}, "__new_primary_file_list_output_tab|batch_tab_000000.tabular__": {"id": "4048439501a9649e", "src": "hda", "uuid": "38fd8726-c428-4104-a7de-c8e09c1445ba"}}, "output_collections": {"list_output_tab": {"id": "78e6f5152b1d49ec", "src": "hdca"}}, "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": "2023-10-24 12:52:04", "plugin": "core", "name": "end_epoch", "raw_value": "1698151924.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 12:52:04", "plugin": "core", "name": "start_epoch", "raw_value": "1698151924.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-3", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 3, "time_seconds": 123.21050238609314, "inputs": {"split_parms|input": {"src": "hda", "id": "41998eb1e7c376e1"}, "split_parms|top": "2", "split_parms|split_by|select_mode|chunksize": "2", "split_parms|split_by|select_mode|mode": "chunk", "split_parms|split_by|newfilenames": "batch_tab", "split_parms|split_by|select_allocate|allocate": "batch", "split_parms|split_by|select_split_by": "row", "split_parms|select_ftype": "tabular"}, "job": {"model_class": "Job", "id": "6f1a7ccdcdcc2759", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T12:54:12.460878", "create_time": "2023-10-24T12:52:19.558313", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-n87nf", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/4/d/7/dataset_4d709353-de9a-4d6a-82ee-9563b9be25ee.dat' --ftype 'tabular' --top '2' --by 'row' --chunksize 2 --batch --file_names 'batch_tab' --file_ext 'tabular'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 11, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 1, \"newfilenames\": \"batch_tab\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_mode\": {\"__current_case__\": 0, \"chunksize\": \"2\", \"mode\": \"chunk\"}, \"select_split_by\": \"row\"}, \"top\": \"2\"}"}, "inputs": {"input": {"id": "41998eb1e7c376e1", "src": "hda", "uuid": "4d709353-de9a-4d6a-82ee-9563b9be25ee"}}, "outputs": {"__new_primary_file_list_output_tab|batch_tab_000001.tabular__": {"id": "1408f9de6d7feaa3", "src": "hda", "uuid": "1d23ff92-48bd-4d13-b556-4e5aaa74006b"}, "__new_primary_file_list_output_tab|batch_tab_000000.tabular__": {"id": "8b45f74579ecd00b", "src": "hda", "uuid": "e0ad5d45-00e9-42e0-91bf-76b7ebb52d7a"}}, "output_collections": {"list_output_tab": {"id": "d307f376c9f5099d", "src": "hdca"}}, "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": "2023-10-24 12:54:08", "plugin": "core", "name": "end_epoch", "raw_value": "1698152048.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 12:54:08", "plugin": "core", "name": "start_epoch", "raw_value": "1698152048.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-4", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 4, "time_seconds": 134.21225547790527, "inputs": {"split_parms|input": {"src": "hda", "id": "d6529d98fa4d20e4"}, "split_parms|select_mode|numnew": "24", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "chr", "split_parms|select_allocate|allocate": "batch", "split_parms|select_ftype": "txt"}, "job": {"model_class": "Job", "id": "5e9469789eeb70d1", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T12:56:20.439960", "create_time": "2023-10-24T12:54:23.208763", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-jgxh8", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/c/4/1/dataset_c41ddb76-4918-4a07-b8f8-a3d0efb7a214.dat' --ftype 'txt' --numnew '24' --batch --file_names 'chr' --file_ext 'txt'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 5, \"input\": {\"values\": [{\"id\": 14, \"src\": \"hda\"}]}, \"newfilenames\": \"chr\", \"select_allocate\": {\"__current_case__\": 1, \"allocate\": \"batch\"}, \"select_ftype\": \"txt\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"24\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"txt\""}, "inputs": {"input": {"id": "d6529d98fa4d20e4", "src": "hda", "uuid": "c41ddb76-4918-4a07-b8f8-a3d0efb7a214"}}, "outputs": {"__new_primary_file_list_output_txt|chr_000023.txt__": {"id": "ec35bec72ddbe584", "src": "hda", "uuid": "17daca4e-0f05-4d40-9230-3d82cb699522"}, "__new_primary_file_list_output_txt|chr_000022.txt__": {"id": "3a88fc208ede802a", "src": "hda", "uuid": "fdb61661-fdb0-43b3-b101-9e5525766566"}, "__new_primary_file_list_output_txt|chr_000021.txt__": {"id": "99b46ab0c011e874", "src": "hda", "uuid": "577c15a1-8c1b-4744-b1cc-ec864671dcba"}, "__new_primary_file_list_output_txt|chr_000020.txt__": {"id": "0d30238634ef1036", "src": "hda", "uuid": "90d19737-6294-4ae3-87f3-500b8d64b795"}, "__new_primary_file_list_output_txt|chr_000019.txt__": {"id": "61c23418ca407c16", "src": "hda", "uuid": "cfae0927-0253-4719-bbd3-1486115b1845"}, "__new_primary_file_list_output_txt|chr_000018.txt__": {"id": "0a921a3874de1b96", "src": "hda", "uuid": "4e0ecfae-7a6e-4333-86de-cbacaa3eb5c0"}, "__new_primary_file_list_output_txt|chr_000017.txt__": {"id": "733e4defa23258f2", "src": "hda", "uuid": "351e250e-0649-4130-ade7-7353c1411348"}, "__new_primary_file_list_output_txt|chr_000016.txt__": {"id": "caeb7889bed8b1e9", "src": "hda", "uuid": "4ca0ac70-d759-46c4-9cfd-c113dbf9a6d8"}, "__new_primary_file_list_output_txt|chr_000015.txt__": {"id": "e4210ace140f89c6", "src": "hda", "uuid": "720f6d2c-a867-4548-b78e-9c804d92894c"}, "__new_primary_file_list_output_txt|chr_000014.txt__": {"id": "38ce598410d419ba", "src": "hda", "uuid": "65fa6087-bb85-487e-a26e-88fc696b756a"}, "__new_primary_file_list_output_txt|chr_000013.txt__": {"id": "798564e7ae325875", "src": "hda", "uuid": "5ade5fbf-8608-4c17-a6ed-4a0e13658051"}, "__new_primary_file_list_output_txt|chr_000012.txt__": {"id": "f4e32b56559dcaad", "src": "hda", "uuid": "a6909419-52c3-4752-9b82-a444946b4212"}, "__new_primary_file_list_output_txt|chr_000011.txt__": {"id": "3fb46099ab1f2343", "src": "hda", "uuid": "af353b49-d2aa-4e78-a240-47ba51f335f1"}, "__new_primary_file_list_output_txt|chr_000010.txt__": {"id": "1e254b8106e95b60", "src": "hda", "uuid": "62ece4f5-2518-442c-9cb5-a0be4412bef9"}, "__new_primary_file_list_output_txt|chr_000009.txt__": {"id": "5dc7a9949ffeb878", "src": "hda", "uuid": "ab355d6d-8209-49b8-b0c5-5d1ac3cf7607"}, "__new_primary_file_list_output_txt|chr_000008.txt__": {"id": "4d36424e8e43b8d9", "src": "hda", "uuid": "260fc2bc-d073-473c-ab85-acbb1c940ec0"}, "__new_primary_file_list_output_txt|chr_000007.txt__": {"id": "05afb11be5b57bdb", "src": "hda", "uuid": "293b308c-8e86-45e7-ac54-01c26f831532"}, "__new_primary_file_list_output_txt|chr_000006.txt__": {"id": "e2b34ac340662f96", "src": "hda", "uuid": "8c128d5e-920f-4452-8950-8e1295cacbbd"}, "__new_primary_file_list_output_txt|chr_000005.txt__": {"id": "d8c45a6ea5797d07", "src": "hda", "uuid": "1321b043-2c02-4116-a1cd-f8198266cc21"}, "__new_primary_file_list_output_txt|chr_000004.txt__": {"id": "0c052697fe8e380d", "src": "hda", "uuid": "925e0988-d2f1-4ca5-b196-91220d0d1bfd"}, "__new_primary_file_list_output_txt|chr_000003.txt__": {"id": "3671510065811f7e", "src": "hda", "uuid": "87af82a0-79b1-445b-a7a2-12a953a10cce"}, "__new_primary_file_list_output_txt|chr_000002.txt__": {"id": "93fcde8a61d133d1", "src": "hda", "uuid": "d948f19f-c049-4b25-996d-85eb7881847c"}, "__new_primary_file_list_output_txt|chr_000001.txt__": {"id": "dcad3eccc186af55", "src": "hda", "uuid": "56d68825-7556-439a-8196-ac3394eed44b"}, "__new_primary_file_list_output_txt|chr_000000.txt__": {"id": "90cb9477be57fb80", "src": "hda", "uuid": "a0ddc075-e24a-4bcc-99ae-068e9b56d545"}}, "output_collections": {"list_output_txt": {"id": "95eaf33b84196d13", "src": "hdca"}}, "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": "2023-10-24 12:56:15", "plugin": "core", "name": "end_epoch", "raw_value": "1698152175.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 12:56:15", "plugin": "core", "name": "start_epoch", "raw_value": "1698152175.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-5", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 5, "time_seconds": 128.08645009994507, "inputs": {"split_parms|input": {"src": "hda", "id": "fdf91bf8a8f32f35"}, "split_parms|top": "1", "split_parms|split_by|id_col": "10", "split_parms|split_by|match_regex": "(.*)\\.mgf", "split_parms|split_by|sub_regex": "\\1.tab", "split_parms|split_by|select_split_by": "col", "split_parms|select_ftype": "tabular"}, "job": {"model_class": "Job", "id": "8b45f74579ecd00b", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T12:58:34.265600", "create_time": "2023-10-24T12:56:37.637481", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-fk8jl", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/e/f/0/dataset_ef08fdb2-ba33-43d1-bca6-a97cce87dc2c.dat' --ftype 'tabular' --top '1' --by 'col' --id_column '10' --match '(.*)__backslash__.mgf' --sub '__backslash__1.tab'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 39, \"src\": \"hda\"}]}, \"select_ftype\": \"tabular\", \"split_by\": {\"__current_case__\": 0, \"id_col\": \"10\", \"match_regex\": \"(.*)\\\\.mgf\", \"select_split_by\": \"col\", \"sub_regex\": \"\\\\1.tab\"}, \"top\": \"1\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"tabular\""}, "inputs": {"input": {"id": "fdf91bf8a8f32f35", "src": "hda", "uuid": "ef08fdb2-ba33-43d1-bca6-a97cce87dc2c"}}, "outputs": {"__new_primary_file_list_output_tab|file1.tab__": {"id": "a8f83ae8df4c8e27", "src": "hda", "uuid": "e2c7713f-83d8-49bc-af6a-a920defdfe42"}, "__new_primary_file_list_output_tab|file2.tab__": {"id": "b41492b5fb13d14e", "src": "hda", "uuid": "aba1ff81-469a-4759-b829-4046f27fa24a"}, "__new_primary_file_list_output_tab|file3.tab__": {"id": "6fd968aa0d679677", "src": "hda", "uuid": "b7992cfd-5f1c-435f-939a-6053582223df"}, "__new_primary_file_list_output_tab|file4.tab__": {"id": "f93a058fae9ce79a", "src": "hda", "uuid": "81051aee-60c4-49dd-a358-2a3315232caf"}}, "output_collections": {"list_output_tab": {"id": "bc11060a229d1ae8", "src": "hdca"}}, "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": "2023-10-24 12:58:30", "plugin": "core", "name": "end_epoch", "raw_value": "1698152310.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 12:58:29", "plugin": "core", "name": "start_epoch", "raw_value": "1698152309.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-6", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 6, "time_seconds": 133.65934586524963, "inputs": {"split_parms|input": {"src": "hda", "id": "bbbb1b84556c6414"}, "split_parms|select_mode|numnew": "3", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "demo", "split_parms|select_ftype": "mgf"}, "job": {"model_class": "Job", "id": "d6529d98fa4d20e4", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:00:48.566139", "create_time": "2023-10-24T12:58:46.122261", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-tdkq7", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/d/a/4/dataset_da4856c8-b2e2-4532-bd44-38d2d8008140.dat' --ftype 'mgf' --numnew '3' --file_names 'demo' --file_ext 'mgf'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 44, \"src\": \"hda\"}]}, \"newfilenames\": \"demo\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"mgf\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"3\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"mgf\""}, "inputs": {"input": {"id": "bbbb1b84556c6414", "src": "hda", "uuid": "da4856c8-b2e2-4532-bd44-38d2d8008140"}}, "outputs": {"__new_primary_file_list_output_mgf|demo_000000.mgf__": {"id": "93e3c9072d073bed", "src": "hda", "uuid": "89da5f7d-bf0b-457c-ad8f-57913cf0b280"}, "__new_primary_file_list_output_mgf|demo_000001.mgf__": {"id": "e654ca0c4f8579a1", "src": "hda", "uuid": "62405309-6448-4b6d-905a-9c06964441f4"}, "__new_primary_file_list_output_mgf|demo_000002.mgf__": {"id": "104bcefc6805908c", "src": "hda", "uuid": "86c413e4-3878-4250-bc46-4ce4a54d43f7"}}, "output_collections": {"list_output_mgf": {"id": "1061adec31e025b4", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:00:44", "plugin": "core", "name": "start_epoch", "raw_value": "1698152444.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:00:44", "plugin": "core", "name": "end_epoch", "raw_value": "1698152444.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-7", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 7, "time_seconds": 128.0825343132019, "inputs": {"split_parms|input": {"src": "hda", "id": "7870a7723c8d7f0a"}, "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "test", "split_parms|select_ftype": "fasta"}, "job": {"model_class": "Job", "id": "dcad3eccc186af55", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:02:56.829238", "create_time": "2023-10-24T13:00:59.441059", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-xp7b7", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/c/d/d/dataset_cdd00df7-cf13-44a2-9cf5-76f990fbe34d.dat' --ftype 'fasta' --numnew '2' --file_names 'test' --file_ext 'fasta'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 3, \"input\": {\"values\": [{\"id\": 48, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"fasta\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"input": {"id": "7870a7723c8d7f0a", "src": "hda", "uuid": "cdd00df7-cf13-44a2-9cf5-76f990fbe34d"}}, "outputs": {"__new_primary_file_list_output_fasta|test_000000.fasta__": {"id": "6a6303a31758e35c", "src": "hda", "uuid": "8eb6705e-979c-4cc6-a021-905a3a4a5127"}, "__new_primary_file_list_output_fasta|test_000001.fasta__": {"id": "3b992805e43011c2", "src": "hda", "uuid": "d51ebe94-3839-474a-8e6e-06e3a37f0f7f"}}, "output_collections": {"list_output_fasta": {"id": "6f1a7ccdcdcc2759", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:02:52", "plugin": "core", "name": "start_epoch", "raw_value": "1698152572.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:02:53", "plugin": "core", "name": "end_epoch", "raw_value": "1698152573.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-8", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 8, "time_seconds": 127.21630334854126, "inputs": {"split_parms|input": {"src": "hda", "id": "b80f7e3aa89e8c14"}, "split_parms|select_mode|chunksize": "3", "split_parms|select_mode|mode": "chunk", "split_parms|newfilenames": "test", "split_parms|select_ftype": "fasta"}, "job": {"model_class": "Job", "id": "3671510065811f7e", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:05:04.239753", "create_time": "2023-10-24T13:03:07.676185", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-zz4lx", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/b/3/1/dataset_b31b6387-15e6-4c09-8297-ea39acf91766.dat' --ftype 'fasta' --chunksize 3 --file_names 'test' --file_ext 'fasta'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 3, \"input\": {\"values\": [{\"id\": 51, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"fasta\", \"select_mode\": {\"__current_case__\": 0, \"chunksize\": \"3\", \"mode\": \"chunk\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"input": {"id": "b80f7e3aa89e8c14", "src": "hda", "uuid": "b31b6387-15e6-4c09-8297-ea39acf91766"}}, "outputs": {"__new_primary_file_list_output_fasta|test_000000.fasta__": {"id": "65a86f489fbc8436", "src": "hda", "uuid": "16f09254-13e4-4251-b379-77a8897c4b16"}, "__new_primary_file_list_output_fasta|test_000001.fasta__": {"id": "3d9b326f0a2de686", "src": "hda", "uuid": "6cff2be5-daf2-41be-bd33-ba4a86266f24"}}, "output_collections": {"list_output_fasta": {"id": "4048439501a9649e", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:04:58", "plugin": "core", "name": "start_epoch", "raw_value": "1698152698.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:04:58", "plugin": "core", "name": "end_epoch", "raw_value": "1698152698.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "split_file_to_collection/0.5.0-9", "has_data": true, "data": {"tool_id": "split_file_to_collection", "tool_version": "0.5.0", "test_index": 9, "time_seconds": 131.44726181030273, "inputs": {"split_parms|input": {"src": "hda", "id": "7f96254824b4e9d2"}, "split_parms|select_mode|numnew": "2", "split_parms|select_mode|mode": "numnew", "split_parms|newfilenames": "test", "split_parms|select_ftype": "fastq"}, "job": {"model_class": "Job", "id": "d8c45a6ea5797d07", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:07:15.621421", "create_time": "2023-10-24T13:05:14.985203", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "history_id": "639c57257ba4f009", "external_id": "gxy-ptl62", "command_line": "mkdir ./out && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/galaxy/server/database/objects/9/9/2/dataset_9923c92e-e02a-4201-b712-4a153114a42b.dat' --ftype 'fastq' --numnew '2' --file_names 'test' --file_ext 'fastq'", "traceback": null, "params": {"split_parms": "{\"__current_case__\": 2, \"input\": {\"values\": [{\"id\": 54, \"src\": \"hda\"}]}, \"newfilenames\": \"test\", \"select_allocate\": {\"__current_case__\": 2, \"allocate\": \"byrow\"}, \"select_ftype\": \"fastq\", \"select_mode\": {\"__current_case__\": 1, \"mode\": \"numnew\", \"numnew\": \"2\"}}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input": {"id": "7f96254824b4e9d2", "src": "hda", "uuid": "9923c92e-e02a-4201-b712-4a153114a42b"}}, "outputs": {"__new_primary_file_list_output_fastq|test_000001.fastq__": {"id": "b3e0a0036c2c5d5a", "src": "hda", "uuid": "5c31ff57-0d1b-4c48-b650-34bfe7419c82"}, "__new_primary_file_list_output_fastq|test_000000.fastq__": {"id": "36669d7f8bd179b8", "src": "hda", "uuid": "7a48b7f2-d0ec-440a-8e1d-7330c9fdb6ef"}}, "output_collections": {"list_output_fastq": {"id": "5e9469789eeb70d1", "src": "hdca"}}, "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:07:10", "plugin": "core", "name": "start_epoch", "raw_value": "1698152830.0000000"}, {"title": "Job End Time", "value": "2023-10-24 13:07:10", "plugin": "core", "name": "end_epoch", "raw_value": "1698152830.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "unicycler/0.4.8.0-0", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.4.8.0", "test_index": 0, "time_seconds": 246.70175290107727, "inputs": {"paired_unpaired|fastq_input1": {"src": "hda", "id": "db5d351431b61037"}, "paired_unpaired|fastq_input2": {"src": "hda", "id": "04c096c2fd37e98f"}, "paired_unpaired|fastq_input_selector": "paired", "mode": "normal", "min_fasta_length": "100", "linear_seqs": "0", "spades|no_correct": true, "spades|min_kmer_frac": "0.2", "spades|max_kmer_frac": "0.95", "spades|kmer_count": "10", "spades|depth_filter": "0.25", "rotation|no_rotate": false, "rotation|start_gene_id": "90", "rotation|start_gene_cov": "95", "pilon|no_pilon": false, "pilon|min_polish_size": "1000", "graph_clean|min_component_size": "1000", "graph_clean|min_dead_end_size": "1000", "lr_align|scores": "3,-6,-5,-2"}, "job": {"model_class": "Job", "id": "450365f003f18a7f", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:34:29.837557", "create_time": "2023-10-24T14:30:36.253131", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0", "history_id": "639c57257ba4f009", "external_id": "gxy-44zzh", "command_line": "ln -s '/galaxy/server/database/objects/d/a/2/dataset_da2aef42-a1a1-447e-947c-848afe30e352.dat' fq1.fastq && ln -s '/galaxy/server/database/objects/b/0/9/dataset_b094c395-0daa-48ad-88d2-77ff7e5411bc.dat' fq2.fastq && pilon=`pilon --jar_dir` && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 --pilon_path $pilon -1 'fq1.fastq' -2 'fq2.fastq' --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --no_correct --min_kmer_frac '0.2' --max_kmer_frac '0.95' --kmer_count '10' --depth_filter '0.25' --start_gene_id '90.0' --start_gene_cov '95.0' --min_polish_size '1000' --min_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"scores\": \"3,-6,-5,-2\"}", "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", "pilon": "{\"min_polish_size\": \"1000\", \"no_pilon\": \"false\"}", "rotation": "{\"no_rotate\": \"false\", \"start_gene_cov\": \"95.0\", \"start_gene_id\": \"90.0\", \"start_genes\": null}", "spades": "{\"depth_filter\": \"0.25\", \"kmer_count\": \"10\", \"kmers\": \"\", \"largest_component\": \"false\", \"max_kmer_frac\": \"0.95\", \"min_kmer_frac\": \"0.2\", \"no_correct\": \"true\"}", "min_anchor_seg_len": "\"\"", "linear_seqs": "\"0\"", "min_fasta_length": "\"100\"", "mode": "\"normal\"", "long": null, "paired_unpaired": "{\"__current_case__\": 0, \"fastq_input1\": {\"values\": [{\"id\": 156, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 157, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"paired\"}"}, "inputs": {"fastq_input2": {"id": "04c096c2fd37e98f", "src": "hda", "uuid": "b094c395-0daa-48ad-88d2-77ff7e5411bc"}, "fastq_input1": {"id": "db5d351431b61037", "src": "hda", "uuid": "da2aef42-a1a1-447e-947c-848afe30e352"}}, "outputs": {"assembly_graph": {"id": "a8c9e8d3ad346a3f", "src": "hda", "uuid": "d52fd68a-8cfe-4fa7-a255-9747d71eafab"}, "assembly": {"id": "00bb3cbea928792a", "src": "hda", "uuid": "e31524b8-bf77-494a-b8fa-4e70e8ae8ae7"}}, "output_collections": {}, "tool_stdout": "\nStarting Unicycler (2023-10-24 14:32:45)\n Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you\nprovided only short reads, Unicycler will essentially function as a SPAdes-\noptimiser. It will try many k-mer sizes, choose the best based on contig length\nand graph connectivity, and scaffold the graph using SPAdes repeat resolution.\n For more information, please see https://github.com/rrwick/Unicycler\n\nCommand: /usr/local/bin/unicycler -t 4 -o ./ --verbosity 3 --pilon_path /usr/local/share/pilon-1.24-0/pilon.jar -1 fq1.fastq -2 fq2.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --no_correct --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2\n\nUnicycler version: v0.4.8\nUsing 4 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/95/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 3.14.1 good /usr/local/bin/spades.py \n racon not used \n makeblastdb 2.12.0+ good /usr/local/bin/makeblastdb \n tblastn 2.12.0+ good /usr/local/bin/tblastn \n bowtie2-build 2.4.4 good /usr/local/bin/bowtie2-build \n bowtie2 2.4.4 good /usr/local/bin/bowtie2 \n samtools 1.14 good /usr/local/bin/samtools \n java 11.0.9.1-internal good /usr/local/bin/java \n pilon 1.24 good /usr/local/share/pilon-1.24-0/pilon.jar\n bcftools not used \n\n\nChoosing k-mer range for assembly (2023-10-24 14:32:47)\n Unicycler chooses a k-mer range for SPAdes based on the length of the input\nreads. It uses a wide range of many k-mer sizes to maximise the chance of\nfinding an ideal assembly.\n\nSPAdes maximum k-mer: 127\nMedian read length: 251\nK-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127\n\n\nSPAdes assemblies (2023-10-24 14:32:47)\n Unicycler now uses SPAdes to assemble the short reads. It scores the\nassembly graph for each k-mer using the number of contigs (fewer is better) and\nthe number of dead ends (fewer is better). The score function is 1/(c*(d+2)),\nwhere c is the contig count and d is the dead end count.\n\n== Warning == No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly -k 27,47,63,77,89,99,107,115,121,127 --threads 4 --only-assembler -1 /galaxy/server/database/jobs_directory/000/95/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/95/working/fq2.fastq\n\nSystem information:\n SPAdes version: 3.14.1\n Python version: 3.9.9\n OS: Linux-5.10.176+-x86_64-with-glibc2.28\nOutput dir: /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Standard mode\n For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/95/working/fq1.fastq']\n right reads: ['/galaxy/server/database/jobs_directory/000/95/working/fq2.fastq']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27, 47, 63, 77, 89, 99, 107, 115, 121, 127]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/tmp\n Threads: 4\n Memory limit (in Gb): 78\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/spades.log\n/galaxy/server/database/jobs_directory/000/95/working/fq1.fastq: max reads length: 251\n/galaxy/server/database/jobs_directory/000/95/working/fq2.fastq: max reads length: 251\nReads length: 251\n===== Before start started.\n===== Assembling started.\n===== K27 started.\n== Running: /usr/local/bin/spades-core /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K27/configs/config.info\nWARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is tmp_contigs.fasta\n 0:00:00.000 5M / 20M INFO General (main.cpp : 75) Loaded config from /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K27/configs/config.info\n 0:00:00.000 5M / 20M INFO General (memory_limit.cpp : 49) Memory limit set to 78 Gb\n 0:00:00.000 5M / 20M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 5M / 20M INFO General (main.cpp : 86) Maximum k-mer length: 128\n 0:00:00.000 5M / 20M INFO General (main.cpp : 87) Assembling dataset (/galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/dataset.info) with K=27\n 0:00:00.000 5M / 20M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 4\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 194) SPAdes started\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0\n 0:00:00.000 5M / 20M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 73) Converting paired reads\n 0:00:00.102 89M / 89M INFO General (binary_converter.cpp : 111) 7925 reads written\n 0:00:00.103 65M / 65M INFO General (read_converter.cpp : 81) Converting single reads\n 0:00:00.105 75M / 75M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.105 75M / 75M INFO General (read_converter.cpp : 87) Converting merged reads\n 0:00:00.107 75M / 75M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.159 26M / 29M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction\n 0:00:00.172 26M / 29M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.173 26M / 29M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.173 26M / 29M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting\n 0:00:00.174 26M / 29M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 4 threads. This might take a while.\n 0:00:00.175 26M / 29M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.175 26M / 29M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49995 Gb\n 0:00:00.175 26M / 29M INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304\n 0:00:00.409 44M / 57M INFO General (kmer_splitters.hpp : 293) Used 31700 reads\n 0:00:00.410 44M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:00.491 44M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 35249 kmers in total.\n 0:00:00.492 44M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:00.562 44M / 57M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction\n 0:00:00.564 44M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:00.564 44M / 57M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 4 threads. This might take a while.\n 0:00:00.565 44M / 57M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.565 44M / 57M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49992 Gb\n 0:00:00.566 44M / 57M INFO General (kmer_splitters.hpp : 97) Using cell size of 1048576\n 0:00:01.285 3G / 3G INFO General (kmer_splitters.hpp : 364) Processed 35249 kmers\n 0:00:01.286 3G / 3G INFO General (kmer_splitters.hpp : 369) Used 35249 kmers.\n 0:00:01.294 45M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:01.654 45M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 34510 kmers in total.\n 0:00:01.654 45M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:01.886 45M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:01.933 40M / 57M INFO General (kmer_index_builder.hpp : 150) Merging final buckets.\n 0:00:01.975 40M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 24880 bytes occupied (5.7676 bits per kmer).\n 0:00:01.975 40M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers\n 0:00:01.984 40M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.\n 0:00:01.985 40M / 57M INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping\n 0:00:01.986 40M / 57M INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K)\n 0:00:01.986 40M / 57M INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping\n 0:00:01.994 41M / 57M INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 404\n 0:00:01.994 41M / 57M INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 413\n 0:00:01.995 41M / 57M INFO Early tip clipping (early_simplification.hpp : 30) 7414 28-mers were removed by early tip clipper\n 0:00:01.995 41M / 57M INFO General (stage.cpp : 113) PROCEDURE == Condensing graph\n 0:00:01.998 41M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths\n 0:00:02.003 41M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2055 sequences extracted\n 0:00:02.005 41M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops\n 0:00:02.009 41M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected\n 0:00:02.011 41M / 57M INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)\n 0:00:02.011 41M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:02.012 41M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:02.031 42M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 18528 bytes occupied (4.20506 bits per kmer).\n 0:00:02.031 42M / 57M INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.123 42M / 57M INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM\n 0:00:02.126 42M / 57M INFO General (construction.cpp : 505) Processed 4110 edges\n 0:00:02.131 42M / 57M INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding\n 0:00:02.132 42M / 57M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7\n 0:00:02.133 42M / 57M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 695\n 0:00:02.133 42M / 57M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.133 42M / 57M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model\n 0:00:02.214 42M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2\n 0:00:02.419 42M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4\n 0:00:02.908 42M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8\n 0:00:03.472 42M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16\n 0:00:04.437 42M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32\n 0:00:04.437 42M / 57M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:04.438 42M / 57M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1\n 0:00:04.439 42M / 57M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 275\n 0:00:04.439 42M / 57M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 275\n 0:00:04.439 42M / 57M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 5132\n 0:00:04.439 42M / 57M INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 671.577\n 0:00:04.439 42M / 57M INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 275\n 0:00:04.439 42M / 57M INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0\n 0:00:04.439 42M / 57M INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification\n 0:00:04.439 42M / 57M INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning\n 0:00:04.439 42M / 57M INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled\n 0:00:04.440 42M / \n..\nO General (launcher.cpp : 246) Deduplicating paths\n 0:00:06.490 34M / 102M INFO General (launcher.cpp : 250) Paths deduplicated\n 0:00:06.490 34M / 102M INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps\n 0:00:06.490 34M / 102M INFO PEResolver (pe_resolver.hpp : 298) Sorting paths\n 0:00:06.491 34M / 102M INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps\n 0:00:06.491 34M / 102M INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps\n 0:00:06.491 34M / 102M INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps\n 0:00:06.491 34M / 102M INFO PEResolver (pe_resolver.hpp : 308) Splitting paths\n 0:00:06.491 34M / 102M INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths\n 0:00:06.492 34M / 102M INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed\n 0:00:06.492 34M / 102M INFO General (launcher.cpp : 267) Paths finalized\n 0:00:06.492 34M / 102M INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished\n 0:00:06.492 34M / 102M INFO StageManager (stage.cpp : 166) STAGE == Contig Output\n 0:00:06.492 34M / 102M INFO General (contig_output.hpp : 21) Outputting contigs to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/before_rr.fasta\n 0:00:06.500 34M / 102M INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/assembly_graph_with_scaffolds.gfa\n 0:00:06.500 34M / 102M INFO General (contig_output_stage.cpp : 160) Outputting FastG graph to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/assembly_graph.fastg\n 0:00:06.505 34M / 102M INFO General (contig_output_stage.cpp : 190) Breaking scaffolds\n 0:00:06.506 34M / 102M INFO General (contig_output_stage.cpp : 95) Outputting contigs to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/final_contigs.fasta\n 0:00:06.511 34M / 102M INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/final_contigs.paths\n 0:00:06.518 34M / 102M INFO General (contig_output_stage.cpp : 95) Outputting contigs to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/scaffolds.fasta\n 0:00:06.523 34M / 102M INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/scaffolds.paths\n 0:00:06.528 34M / 102M INFO General (contig_output_stage.cpp : 108) Populating GFA with scaffold paths\n 0:00:06.540 34M / 102M INFO General (pipeline.cpp : 259) SPAdes finished\n 0:00:06.544 30M / 102M INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 6 seconds\n===== K127 finished.\n===== Copy files started.\n== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/before_rr.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/before_rr.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/final_contigs.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/contigs.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/strain_graph.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/strain_graph.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/scaffolds.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/scaffolds.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/scaffolds.paths /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/scaffolds.paths /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/final_contigs.paths /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/contigs.paths\n===== Copy files finished.\n===== Assembling finished.\n===== Breaking scaffolds started.\n== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/scaffolds.fasta --misc_dir /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/misc --threshold_for_breaking_scaffolds 3\n===== Breaking scaffolds finished.\n===== Terminate started.\n===== Terminate finished.\n * Assembled contigs are in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/contigs.fasta\n * Assembled scaffolds are in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/scaffolds.fasta\n * Paths in the assembly graph corresponding to the contigs are in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/contigs.paths\n * Paths in the assembly graph corresponding to the scaffolds are in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/scaffolds.paths\n * Assembly graph is in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/assembly_graph.fastg\n * Assembly graph in GFA format is in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa\n======= SPAdes pipeline finished WITH WARNINGS!\n=== Error correction and assembling warnings:\n * 0:00:06.484 35M / 102M WARN General (launcher.cpp : 172) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option.\n======= Warnings saved to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/warnings.log\nSPAdes log can be found here: /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/spades.log\nThank you for using SPAdes!\n\nInsert size mean: 367.3 bp\nInsert size stdev: 37.3 bp\n\n\nCleaning k127 graph\nRepair multi way junctions (2023-10-24 14:33:59)\nFilter by read depth (2023-10-24 14:33:59)\nFilter homopolymer loops (2023-10-24 14:33:59)\nMerge all possible (2023-10-24 14:33:59)\nNormalise read depths (2023-10-24 14:33:59)\nRemove zero length segments (2023-10-24 14:33:59)\nSort link order (2023-10-24 14:33:59)\nGraph cleaning finished (2023-10-24 14:33:59)\nSaving /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2023-10-24 14:33:59)\nFilter by read depth (2023-10-24 14:33:59)\nFilter homopolymer loops (2023-10-24 14:33:59)\nMerge all possible (2023-10-24 14:33:59)\nNormalise read depths (2023-10-24 14:33:59)\nRemove zero length segments (2023-10-24 14:33:59)\nSort link order (2023-10-24 14:33:59)\nGraph cleaning finished (2023-10-24 14:33:59)\nSaving /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/k127_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2023-10-24 14:33:59)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 \n 47 \n 63 \n 77 \n 89 \n 99 \n 107 \n 115 \n 121 \n 127 1 1 5,513 5,513 5,513 0 5.00e-01 <-best\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/\n\n\nDetermining graph multiplicity (2023-10-24 14:33:59)\n Multiplicity is the number of times a sequence occurs in the underlying\nsequence. Single-copy contigs (those with a multiplicity of one, occurring only\nonce in the underlying sequence) are particularly useful.\n Multiplicity determination begins by identifying contigs which are clearly\nsingle-copy because they are of low depth and do not have more than one link\nper side.\n\nMedian depth of 10 longest contigs: 1.00\n\n\nInitial single copy segments:\n 1\n\n Unicycler now uses a greedy algorithm to propagate multiplicity through the\ngraph. For example, if two single-copy contigs merge together, the resulting\ncontig will get a multiplicity of two. When no more propagation is possible,\nadditional single-copy contigs are added and the process is repeated. This\nallows for multiplicity to be correctly assigned to the chromosome (at the\nmedian depth) but also for plasmids (which may be higher or lower in depth).\n\n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n FINDING NEW SINGLE-COPY \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \nREMOVING PROPAGATION TOLERANCE \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n\nSaving /galaxy/server/database/jobs_directory/000/95/working/001_best_spades_graph.gfa\n\n\nCleaning graph (2023-10-24 14:33:59)\n Unicycler now performs various cleaning procedures on the graph to remove\noverlaps and simplify the graph structure. The end result is a graph ready for\nbridging.\n\nGrouping graph edges based on overlap removal\n\r0 / 2 (0.0%)\r1 / 2 (50.0%)\r2 / 2 (100.0%)\n\nRemoving graph overlaps\n\n Bases Bases\n trimmed trimmed\n Segment from from\n number start end\n 1 63 64\nGraph overlaps removed\n\nSaving /galaxy/server/database/jobs_directory/000/95/working/002_overlaps_removed.gfa\n\n Unicycler now selects a set of anchor contigs from the single-copy contigs.\nThese are the contigs which will be connected via bridges to form the final\nassembly.\n\n\n1 anchor segments (5,386 bp) out of 1 total segments (5,386 bp)\n\nAnchor segments:\n 1\n\n\nCreating SPAdes contig bridges (2023-10-24 14:33:59)\n SPAdes uses paired-end information to perform repeat resolution (RR) and\nproduce contigs from the assembly graph. SPAdes saves the graph paths\ncorresponding to these contigs in the contigs.paths file. When one of these\npaths contains two or more anchor contigs, Unicycler can create a bridge from\nthe path.\n\nNo SPAdes contig bridges\n\n\nCreating loop unrolling bridges (2023-10-24 14:33:59)\n When a SPAdes contig path connects an anchor contig with the middle contig\nof a simple loop, Unicycler concludes that the sequences are contiguous (i.e.\nthe loop is not a separate piece of DNA). It then uses the read depth of the\nmiddle and repeat contigs to guess the number of times to traverse the loop and\nmakes a bridge.\n\nNo loop unrolling bridges made\nnone found\n\n\nApplying bridges (2023-10-24 14:33:59)\n Unicycler now applies to the graph in decreasing order of quality. This\nensures that when multiple, contradictory bridges exist, the most supported\noption is used.\n\nBridge type Start -> end Path Quality Result\n\nSaving /galaxy/server/database/jobs_directory/000/95/working/003_bridges_applied.gfa\n\n\nCleaning up leftover segments (2023-10-24 14:33:59)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2023-10-24 14:33:59)\n The assembly is now mostly finished and no more structural changes will be\nmade. Ideally the assembly graph should now have one contig per replicon and no\nerroneous contigs (i.e a complete assembly). If there are more contigs, then\nthe assembly is not complete.\n\nSaving /galaxy/server/database/jobs_directory/000/95/working/004_final_clean.gfa\n\nComponent Segments Links Length N50 Longest segment Status \n 1 1 1 5,386 5,386 5,386 complete\n\n\nPolishing assembly with Pilon (2023-10-24 14:33:59)\n Unicycler now conducts multiple rounds of Pilon in an attempt to repair any\nremaining small-scale errors with the assembly.\n\nAligning reads to find appropriate insert size range...\n bowtie2-build 0_insert_size_check.fasta 0_insert_size_check.fasta\n bowtie2 -1 /galaxy/server/database/jobs_directory/000/95/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/95/working/fq2.fastq -x 0_insert_size_check.fasta --fast --threads 4 -I 0 -X 5000 -S 0_alignments.sam\nInsert size 1st percentile: 263\nInsert size 99th percentile: 450\n\nPilon polish round 1\n bowtie2-build 1_polish_input.fasta 1_polish_input.fasta\n bowtie2 --local --very-sensitive-local --threads 4 -I 263 -X 450 -x 1_polish_input.fasta -S 1_paired_alignments.sam -1 /galaxy/server/database/jobs_directory/000/95/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/95/working/fq2.fastq\n samtools sort -@ 4 -o 1_paired_alignments.bam -O bam -T temp 1_paired_alignments.sam\n samtools index 1_paired_alignments.bam\n java -jar /usr/local/share/pilon-1.24-0/pilon.jar --genome 1_polish_input.fasta --changes --output 1_pilon --outdir /galaxy/server/database/jobs_directory/000/95/working/pilon_polish --fix bases --frags 1_paired_alignments.bam\nNo Pilon changes\n\nSaving /galaxy/server/database/jobs_directory/000/95/working/005_polished.gfa\n\n\nRotating completed replicons (2023-10-24 14:34:05)\n Any completed circular contigs (i.e. single contigs which have one link\nconnecting end to start) can have their start position changed without altering\nthe sequence. For consistency, Unicycler now searches for a starting gene (dnaA\nor repA) in each such contig, and if one is found, the contig is rotated to\nstart with that gene on the forward strand.\n\nSegment 1:\n makeblastdb -dbtype nucl -in replicon.fasta\n tblastn -db replicon.fasta -query /usr/local/lib/python3.9/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1\n\nSegment Length Depth Starting gene Position Strand Identity Coverage\n 1 5,386 1.00x none found \n\n\nAssembly complete (2023-10-24 14:34:20)\nSaving /galaxy/server/database/jobs_directory/000/95/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/95/working/assembly.fasta\n\n", "tool_stderr": "tput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\n", "job_stdout": "", "job_stderr": "", "stderr": "tput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\n", "stdout": "\nStarting Unicycler (2023-10-24 14:32:45)\n Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you\nprovided only short reads, Unicycler will essentially function as a SPAdes-\noptimiser. It will try many k-mer sizes, choose the best based on contig length\nand graph connectivity, and scaffold the graph using SPAdes repeat resolution.\n For more information, please see https://github.com/rrwick/Unicycler\n\nCommand: /usr/local/bin/unicycler -t 4 -o ./ --verbosity 3 --pilon_path /usr/local/share/pilon-1.24-0/pilon.jar -1 fq1.fastq -2 fq2.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --no_correct --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2\n\nUnicycler version: v0.4.8\nUsing 4 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/95/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 3.14.1 good /usr/local/bin/spades.py \n racon not used \n makeblastdb 2.12.0+ good /usr/local/bin/makeblastdb \n tblastn 2.12.0+ good /usr/local/bin/tblastn \n bowtie2-build 2.4.4 good /usr/local/bin/bowtie2-build \n bowtie2 2.4.4 good /usr/local/bin/bowtie2 \n samtools 1.14 good /usr/local/bin/samtools \n java 11.0.9.1-internal good /usr/local/bin/java \n pilon 1.24 good /usr/local/share/pilon-1.24-0/pilon.jar\n bcftools not used \n\n\nChoosing k-mer range for assembly (2023-10-24 14:32:47)\n Unicycler chooses a k-mer range for SPAdes based on the length of the input\nreads. It uses a wide range of many k-mer sizes to maximise the chance of\nfinding an ideal assembly.\n\nSPAdes maximum k-mer: 127\nMedian read length: 251\nK-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127\n\n\nSPAdes assemblies (2023-10-24 14:32:47)\n Unicycler now uses SPAdes to assemble the short reads. It scores the\nassembly graph for each k-mer using the number of contigs (fewer is better) and\nthe number of dead ends (fewer is better). The score function is 1/(c*(d+2)),\nwhere c is the contig count and d is the dead end count.\n\n== Warning == No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly -k 27,47,63,77,89,99,107,115,121,127 --threads 4 --only-assembler -1 /galaxy/server/database/jobs_directory/000/95/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/95/working/fq2.fastq\n\nSystem information:\n SPAdes version: 3.14.1\n Python version: 3.9.9\n OS: Linux-5.10.176+-x86_64-with-glibc2.28\nOutput dir: /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Standard mode\n For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/95/working/fq1.fastq']\n right reads: ['/galaxy/server/database/jobs_directory/000/95/working/fq2.fastq']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27, 47, 63, 77, 89, 99, 107, 115, 121, 127]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/tmp\n Threads: 4\n Memory limit (in Gb): 78\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/spades.log\n/galaxy/server/database/jobs_directory/000/95/working/fq1.fastq: max reads length: 251\n/galaxy/server/database/jobs_directory/000/95/working/fq2.fastq: max reads length: 251\nReads length: 251\n===== Before start started.\n===== Assembling started.\n===== K27 started.\n== Running: /usr/local/bin/spades-core /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K27/configs/config.info\nWARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is tmp_contigs.fasta\n 0:00:00.000 5M / 20M INFO General (main.cpp : 75) Loaded config from /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K27/configs/config.info\n 0:00:00.000 5M / 20M INFO General (memory_limit.cpp : 49) Memory limit set to 78 Gb\n 0:00:00.000 5M / 20M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 5M / 20M INFO General (main.cpp : 86) Maximum k-mer length: 128\n 0:00:00.000 5M / 20M INFO General (main.cpp : 87) Assembling dataset (/galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/dataset.info) with K=27\n 0:00:00.000 5M / 20M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 4\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 194) SPAdes started\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0\n 0:00:00.000 5M / 20M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 73) Converting paired reads\n 0:00:00.102 89M / 89M INFO General (binary_converter.cpp : 111) 7925 reads written\n 0:00:00.103 65M / 65M INFO General (read_converter.cpp : 81) Converting single reads\n 0:00:00.105 75M / 75M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.105 75M / 75M INFO General (read_converter.cpp : 87) Converting merged reads\n 0:00:00.107 75M / 75M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.159 26M / 29M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction\n 0:00:00.172 26M / 29M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.173 26M / 29M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.173 26M / 29M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting\n 0:00:00.174 26M / 29M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 4 threads. This might take a while.\n 0:00:00.175 26M / 29M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.175 26M / 29M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49995 Gb\n 0:00:00.175 26M / 29M INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304\n 0:00:00.409 44M / 57M INFO General (kmer_splitters.hpp : 293) Used 31700 reads\n 0:00:00.410 44M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:00.491 44M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 35249 kmers in total.\n 0:00:00.492 44M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:00.562 44M / 57M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction\n 0:00:00.564 44M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:00.564 44M / 57M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 4 threads. This might take a while.\n 0:00:00.565 44M / 57M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.565 44M / 57M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49992 Gb\n 0:00:00.566 44M / 57M INFO General (kmer_splitters.hpp : 97) Using cell size of 1048576\n 0:00:01.285 3G / 3G INFO General (kmer_splitters.hpp : 364) Processed 35249 kmers\n 0:00:01.286 3G / 3G INFO General (kmer_splitters.hpp : 369) Used 35249 kmers.\n 0:00:01.294 45M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:01.654 45M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 34510 kmers in total.\n 0:00:01.654 45M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:01.886 45M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:01.933 40M / 57M INFO General (kmer_index_builder.hpp : 150) Merging final buckets.\n 0:00:01.975 40M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 24880 bytes occupied (5.7676 bits per kmer).\n 0:00:01.975 40M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers\n 0:00:01.984 40M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.\n 0:00:01.985 40M / 57M INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping\n 0:00:01.986 40M / 57M INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K)\n 0:00:01.986 40M / 57M INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping\n 0:00:01.994 41M / 57M INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 404\n 0:00:01.994 41M / 57M INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 413\n 0:00:01.995 41M / 57M INFO Early tip clipping (early_simplification.hpp : 30) 7414 28-mers were removed by early tip clipper\n 0:00:01.995 41M / 57M INFO General (stage.cpp : 113) PROCEDURE == Condensing graph\n 0:00:01.998 41M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths\n 0:00:02.003 41M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2055 sequences extracted\n 0:00:02.005 41M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops\n 0:00:02.009 41M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected\n 0:00:02.011 41M / 57M INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)\n 0:00:02.011 41M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:02.012 41M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:02.031 42M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 18528 bytes occupied (4.20506 bits per kmer).\n 0:00:02.031 42M / 57M INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.123 42M / 57M INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM\n 0:00:02.126 42M / 57M INFO General (construction.cpp : 505) Processed 4110 edges\n 0:00:02.131 42M / 57M INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding\n 0:00:02.132 42M / 57M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7\n 0:00:02.133 42M / 57M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 695\n 0:00:02.133 42M / 57M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.133 42M / 57M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model\n 0:00:02.214 42M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2\n 0:00:02.419 42M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4\n 0:00:02.908 42M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8\n 0:00:03.472 42M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16\n 0:00:04.437 42M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32\n 0:00:04.437 42M / 57M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:04.438 42M / 57M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1\n 0:00:04.439 42M / 57M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 275\n 0:00:04.439 42M / 57M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 275\n 0:00:04.439 42M / 57M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 5132\n 0:00:04.439 42M / 57M INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 671.577\n 0:00:04.439 42M / 57M INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 275\n 0:00:04.439 42M / 57M INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0\n 0:00:04.439 42M / 57M INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification\n 0:00:04.439 42M / 57M INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning\n 0:00:04.439 42M / 57M INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled\n 0:00:04.440 42M / \n..\nO General (launcher.cpp : 246) Deduplicating paths\n 0:00:06.490 34M / 102M INFO General (launcher.cpp : 250) Paths deduplicated\n 0:00:06.490 34M / 102M INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps\n 0:00:06.490 34M / 102M INFO PEResolver (pe_resolver.hpp : 298) Sorting paths\n 0:00:06.491 34M / 102M INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps\n 0:00:06.491 34M / 102M INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps\n 0:00:06.491 34M / 102M INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps\n 0:00:06.491 34M / 102M INFO PEResolver (pe_resolver.hpp : 308) Splitting paths\n 0:00:06.491 34M / 102M INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths\n 0:00:06.492 34M / 102M INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed\n 0:00:06.492 34M / 102M INFO General (launcher.cpp : 267) Paths finalized\n 0:00:06.492 34M / 102M INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished\n 0:00:06.492 34M / 102M INFO StageManager (stage.cpp : 166) STAGE == Contig Output\n 0:00:06.492 34M / 102M INFO General (contig_output.hpp : 21) Outputting contigs to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/before_rr.fasta\n 0:00:06.500 34M / 102M INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/assembly_graph_with_scaffolds.gfa\n 0:00:06.500 34M / 102M INFO General (contig_output_stage.cpp : 160) Outputting FastG graph to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/assembly_graph.fastg\n 0:00:06.505 34M / 102M INFO General (contig_output_stage.cpp : 190) Breaking scaffolds\n 0:00:06.506 34M / 102M INFO General (contig_output_stage.cpp : 95) Outputting contigs to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/final_contigs.fasta\n 0:00:06.511 34M / 102M INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/final_contigs.paths\n 0:00:06.518 34M / 102M INFO General (contig_output_stage.cpp : 95) Outputting contigs to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/scaffolds.fasta\n 0:00:06.523 34M / 102M INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/scaffolds.paths\n 0:00:06.528 34M / 102M INFO General (contig_output_stage.cpp : 108) Populating GFA with scaffold paths\n 0:00:06.540 34M / 102M INFO General (pipeline.cpp : 259) SPAdes finished\n 0:00:06.544 30M / 102M INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 6 seconds\n===== K127 finished.\n===== Copy files started.\n== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/before_rr.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/before_rr.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/final_contigs.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/contigs.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/strain_graph.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/strain_graph.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/scaffolds.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/scaffolds.fasta /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/scaffolds.paths /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/scaffolds.paths /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/K127/final_contigs.paths /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/contigs.paths\n===== Copy files finished.\n===== Assembling finished.\n===== Breaking scaffolds started.\n== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/scaffolds.fasta --misc_dir /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/misc --threshold_for_breaking_scaffolds 3\n===== Breaking scaffolds finished.\n===== Terminate started.\n===== Terminate finished.\n * Assembled contigs are in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/contigs.fasta\n * Assembled scaffolds are in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/scaffolds.fasta\n * Paths in the assembly graph corresponding to the contigs are in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/contigs.paths\n * Paths in the assembly graph corresponding to the scaffolds are in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/scaffolds.paths\n * Assembly graph is in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/assembly_graph.fastg\n * Assembly graph in GFA format is in /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa\n======= SPAdes pipeline finished WITH WARNINGS!\n=== Error correction and assembling warnings:\n * 0:00:06.484 35M / 102M WARN General (launcher.cpp : 172) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option.\n======= Warnings saved to /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/warnings.log\nSPAdes log can be found here: /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/assembly/spades.log\nThank you for using SPAdes!\n\nInsert size mean: 367.3 bp\nInsert size stdev: 37.3 bp\n\n\nCleaning k127 graph\nRepair multi way junctions (2023-10-24 14:33:59)\nFilter by read depth (2023-10-24 14:33:59)\nFilter homopolymer loops (2023-10-24 14:33:59)\nMerge all possible (2023-10-24 14:33:59)\nNormalise read depths (2023-10-24 14:33:59)\nRemove zero length segments (2023-10-24 14:33:59)\nSort link order (2023-10-24 14:33:59)\nGraph cleaning finished (2023-10-24 14:33:59)\nSaving /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2023-10-24 14:33:59)\nFilter by read depth (2023-10-24 14:33:59)\nFilter homopolymer loops (2023-10-24 14:33:59)\nMerge all possible (2023-10-24 14:33:59)\nNormalise read depths (2023-10-24 14:33:59)\nRemove zero length segments (2023-10-24 14:33:59)\nSort link order (2023-10-24 14:33:59)\nGraph cleaning finished (2023-10-24 14:33:59)\nSaving /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/k127_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2023-10-24 14:33:59)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 \n 47 \n 63 \n 77 \n 89 \n 99 \n 107 \n 115 \n 121 \n 127 1 1 5,513 5,513 5,513 0 5.00e-01 <-best\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/95/working/spades_assembly/\n\n\nDetermining graph multiplicity (2023-10-24 14:33:59)\n Multiplicity is the number of times a sequence occurs in the underlying\nsequence. Single-copy contigs (those with a multiplicity of one, occurring only\nonce in the underlying sequence) are particularly useful.\n Multiplicity determination begins by identifying contigs which are clearly\nsingle-copy because they are of low depth and do not have more than one link\nper side.\n\nMedian depth of 10 longest contigs: 1.00\n\n\nInitial single copy segments:\n 1\n\n Unicycler now uses a greedy algorithm to propagate multiplicity through the\ngraph. For example, if two single-copy contigs merge together, the resulting\ncontig will get a multiplicity of two. When no more propagation is possible,\nadditional single-copy contigs are added and the process is repeated. This\nallows for multiplicity to be correctly assigned to the chromosome (at the\nmedian depth) but also for plasmids (which may be higher or lower in depth).\n\n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n FINDING NEW SINGLE-COPY \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \nREMOVING PROPAGATION TOLERANCE \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n\nSaving /galaxy/server/database/jobs_directory/000/95/working/001_best_spades_graph.gfa\n\n\nCleaning graph (2023-10-24 14:33:59)\n Unicycler now performs various cleaning procedures on the graph to remove\noverlaps and simplify the graph structure. The end result is a graph ready for\nbridging.\n\nGrouping graph edges based on overlap removal\n\r0 / 2 (0.0%)\r1 / 2 (50.0%)\r2 / 2 (100.0%)\n\nRemoving graph overlaps\n\n Bases Bases\n trimmed trimmed\n Segment from from\n number start end\n 1 63 64\nGraph overlaps removed\n\nSaving /galaxy/server/database/jobs_directory/000/95/working/002_overlaps_removed.gfa\n\n Unicycler now selects a set of anchor contigs from the single-copy contigs.\nThese are the contigs which will be connected via bridges to form the final\nassembly.\n\n\n1 anchor segments (5,386 bp) out of 1 total segments (5,386 bp)\n\nAnchor segments:\n 1\n\n\nCreating SPAdes contig bridges (2023-10-24 14:33:59)\n SPAdes uses paired-end information to perform repeat resolution (RR) and\nproduce contigs from the assembly graph. SPAdes saves the graph paths\ncorresponding to these contigs in the contigs.paths file. When one of these\npaths contains two or more anchor contigs, Unicycler can create a bridge from\nthe path.\n\nNo SPAdes contig bridges\n\n\nCreating loop unrolling bridges (2023-10-24 14:33:59)\n When a SPAdes contig path connects an anchor contig with the middle contig\nof a simple loop, Unicycler concludes that the sequences are contiguous (i.e.\nthe loop is not a separate piece of DNA). It then uses the read depth of the\nmiddle and repeat contigs to guess the number of times to traverse the loop and\nmakes a bridge.\n\nNo loop unrolling bridges made\nnone found\n\n\nApplying bridges (2023-10-24 14:33:59)\n Unicycler now applies to the graph in decreasing order of quality. This\nensures that when multiple, contradictory bridges exist, the most supported\noption is used.\n\nBridge type Start -> end Path Quality Result\n\nSaving /galaxy/server/database/jobs_directory/000/95/working/003_bridges_applied.gfa\n\n\nCleaning up leftover segments (2023-10-24 14:33:59)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2023-10-24 14:33:59)\n The assembly is now mostly finished and no more structural changes will be\nmade. Ideally the assembly graph should now have one contig per replicon and no\nerroneous contigs (i.e a complete assembly). If there are more contigs, then\nthe assembly is not complete.\n\nSaving /galaxy/server/database/jobs_directory/000/95/working/004_final_clean.gfa\n\nComponent Segments Links Length N50 Longest segment Status \n 1 1 1 5,386 5,386 5,386 complete\n\n\nPolishing assembly with Pilon (2023-10-24 14:33:59)\n Unicycler now conducts multiple rounds of Pilon in an attempt to repair any\nremaining small-scale errors with the assembly.\n\nAligning reads to find appropriate insert size range...\n bowtie2-build 0_insert_size_check.fasta 0_insert_size_check.fasta\n bowtie2 -1 /galaxy/server/database/jobs_directory/000/95/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/95/working/fq2.fastq -x 0_insert_size_check.fasta --fast --threads 4 -I 0 -X 5000 -S 0_alignments.sam\nInsert size 1st percentile: 263\nInsert size 99th percentile: 450\n\nPilon polish round 1\n bowtie2-build 1_polish_input.fasta 1_polish_input.fasta\n bowtie2 --local --very-sensitive-local --threads 4 -I 263 -X 450 -x 1_polish_input.fasta -S 1_paired_alignments.sam -1 /galaxy/server/database/jobs_directory/000/95/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/95/working/fq2.fastq\n samtools sort -@ 4 -o 1_paired_alignments.bam -O bam -T temp 1_paired_alignments.sam\n samtools index 1_paired_alignments.bam\n java -jar /usr/local/share/pilon-1.24-0/pilon.jar --genome 1_polish_input.fasta --changes --output 1_pilon --outdir /galaxy/server/database/jobs_directory/000/95/working/pilon_polish --fix bases --frags 1_paired_alignments.bam\nNo Pilon changes\n\nSaving /galaxy/server/database/jobs_directory/000/95/working/005_polished.gfa\n\n\nRotating completed replicons (2023-10-24 14:34:05)\n Any completed circular contigs (i.e. single contigs which have one link\nconnecting end to start) can have their start position changed without altering\nthe sequence. For consistency, Unicycler now searches for a starting gene (dnaA\nor repA) in each such contig, and if one is found, the contig is rotated to\nstart with that gene on the forward strand.\n\nSegment 1:\n makeblastdb -dbtype nucl -in replicon.fasta\n tblastn -db replicon.fasta -query /usr/local/lib/python3.9/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1\n\nSegment Length Depth Starting gene Position Strand Identity Coverage\n 1 5,386 1.00x none found \n\n\nAssembly complete (2023-10-24 14:34:20)\nSaving /galaxy/server/database/jobs_directory/000/95/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/95/working/assembly.fasta\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "95.0000000"}, {"title": "Job End Time", "value": "2023-10-24 14:34:20", "plugin": "core", "name": "end_epoch", "raw_value": "1698158060.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:32:45", "plugin": "core", "name": "start_epoch", "raw_value": "1698157965.0000000"}, {"title": "Memory Allocated (MB)", "value": "40000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "40000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "unicycler/0.4.8.0-1", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.4.8.0", "test_index": 1, "time_seconds": 234.00467467308044, "inputs": {"paired_unpaired|fastq_input1": {"src": "hda", "id": "fcd38ca519c462e3"}, "paired_unpaired|fastq_input2": {"src": "hda", "id": "60653eca26084f85"}, "paired_unpaired|fastq_input_selector": "paired", "long": {"src": "hda", "id": "771e98b6241b435e"}, "mode": "normal", "min_fasta_length": "100", "linear_seqs": "0", "spades|no_correct": true, "spades|min_kmer_frac": "0.2", "spades|max_kmer_frac": "0.95", "spades|kmer_count": "10", "spades|depth_filter": "0.25", "rotation|no_rotate": false, "rotation|start_gene_id": "90", "rotation|start_gene_cov": "95", "pilon|no_pilon": false, "pilon|min_polish_size": "1000", "graph_clean|min_component_size": "1000", "graph_clean|min_dead_end_size": "1000", "lr_align|scores": "3,-6,-5,-2"}, "job": {"model_class": "Job", "id": "1b0464b6e7d4db86", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:38:23.907503", "create_time": "2023-10-24T14:34:47.266169", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0", "history_id": "639c57257ba4f009", "external_id": "gxy-sgbjh", "command_line": "ln -s '/galaxy/server/database/objects/2/2/3/dataset_2233458b-f202-41f1-a763-9f2f1e2e9466.dat' fq1.fastq.gz && ln -s '/galaxy/server/database/objects/d/4/2/dataset_d42f181b-2d71-4bde-9c46-f233e02b9353.dat' fq2.fastq.gz && ln -s '/galaxy/server/database/objects/7/5/5/dataset_7550ab22-ba44-4a41-968e-ce79a2dbbba2.dat' 'lr.fasta' && pilon=`pilon --jar_dir` && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 --pilon_path $pilon -1 'fq1.fastq.gz' -2 'fq2.fastq.gz' -l lr.fasta --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --no_correct --min_kmer_frac '0.2' --max_kmer_frac '0.95' --kmer_count '10' --depth_filter '0.25' --start_gene_id '90.0' --start_gene_cov '95.0' --min_polish_size '1000' --min_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"scores\": \"3,-6,-5,-2\"}", "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", "pilon": "{\"min_polish_size\": \"1000\", \"no_pilon\": \"false\"}", "rotation": "{\"no_rotate\": \"false\", \"start_gene_cov\": \"95.0\", \"start_gene_id\": \"90.0\", \"start_genes\": null}", "spades": "{\"depth_filter\": \"0.25\", \"kmer_count\": \"10\", \"kmers\": \"\", \"largest_component\": \"false\", \"max_kmer_frac\": \"0.95\", \"min_kmer_frac\": \"0.2\", \"no_correct\": \"true\"}", "min_anchor_seg_len": "\"\"", "linear_seqs": "\"0\"", "min_fasta_length": "\"100\"", "mode": "\"normal\"", "paired_unpaired": "{\"__current_case__\": 0, \"fastq_input1\": {\"values\": [{\"id\": 160, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 161, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"paired\"}"}, "inputs": {"fastq_input1": {"id": "fcd38ca519c462e3", "src": "hda", "uuid": "2233458b-f202-41f1-a763-9f2f1e2e9466"}, "fastq_input2": {"id": "60653eca26084f85", "src": "hda", "uuid": "d42f181b-2d71-4bde-9c46-f233e02b9353"}, "long": {"id": "771e98b6241b435e", "src": "hda", "uuid": "7550ab22-ba44-4a41-968e-ce79a2dbbba2"}}, "outputs": {"assembly_graph": {"id": "b9c98d5c3b3e9349", "src": "hda", "uuid": "f91eb6a7-5ec5-47a5-8224-c5f21efc9e0a"}, "assembly": {"id": "cbf74323d67c1126", "src": "hda", "uuid": "a2c9afd7-3c70-402c-a8c3-c35634e5b0b5"}}, "output_collections": {}, "tool_stdout": "\nStarting Unicycler (2023-10-24 14:36:36)\n Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you\nprovided both short and long reads, Unicycler will perform a hybrid assembly.\nIt will first use SPAdes to make a short-read assembly graph, and then it will\nuse various methods to scaffold that graph with the long reads.\n For more information, please see https://github.com/rrwick/Unicycler\n\nCommand: /usr/local/bin/unicycler -t 4 -o ./ --verbosity 3 --pilon_path /usr/local/share/pilon-1.24-0/pilon.jar -1 fq1.fastq.gz -2 fq2.fastq.gz -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --no_correct --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2\n\nUnicycler version: v0.4.8\nUsing 4 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/99/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 3.14.1 good /usr/local/bin/spades.py \n racon 1.4.20 good /usr/local/bin/racon \n makeblastdb 2.12.0+ good /usr/local/bin/makeblastdb \n tblastn 2.12.0+ good /usr/local/bin/tblastn \n bowtie2-build 2.4.4 good /usr/local/bin/bowtie2-build \n bowtie2 2.4.4 good /usr/local/bin/bowtie2 \n samtools 1.14 good /usr/local/bin/samtools \n java 11.0.9.1-internal good /usr/local/bin/java \n pilon 1.24 good /usr/local/share/pilon-1.24-0/pilon.jar\n bcftools not used \n\n\nChoosing k-mer range for assembly (2023-10-24 14:36:38)\n Unicycler chooses a k-mer range for SPAdes based on the length of the input\nreads. It uses a wide range of many k-mer sizes to maximise the chance of\nfinding an ideal assembly.\n\nSPAdes maximum k-mer: 127\nMedian read length: 251\nK-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127\n\n\nSPAdes assemblies (2023-10-24 14:36:38)\n Unicycler now uses SPAdes to assemble the short reads. It scores the\nassembly graph for each k-mer using the number of contigs (fewer is better) and\nthe number of dead ends (fewer is better). The score function is 1/(c*(d+2)),\nwhere c is the contig count and d is the dead end count.\n\n== Warning == No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly -k 27,47,63,77,89,99,107,115,121,127 --threads 4 --only-assembler -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz\n\nSystem information:\n SPAdes version: 3.14.1\n Python version: 3.9.9\n OS: Linux-5.10.176+-x86_64-with-glibc2.28\nOutput dir: /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Standard mode\n For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz']\n right reads: ['/galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27, 47, 63, 77, 89, 99, 107, 115, 121, 127]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/tmp\n Threads: 4\n Memory limit (in Gb): 78\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/spades.log\n/galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz: max reads length: 251\n/galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz: max reads length: 251\nReads length: 251\n===== Before start started.\n===== Assembling started.\n===== K27 started.\n== Running: /usr/local/bin/spades-core /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/K27/configs/config.info\nWARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is tmp_contigs.fasta\n 0:00:00.000 5M / 20M INFO General (main.cpp : 75) Loaded config from /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/K27/configs/config.info\n 0:00:00.000 5M / 20M INFO General (memory_limit.cpp : 49) Memory limit set to 78 Gb\n 0:00:00.000 5M / 20M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 5M / 20M INFO General (main.cpp : 86) Maximum k-mer length: 128\n 0:00:00.000 5M / 20M INFO General (main.cpp : 87) Assembling dataset (/galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/dataset.info) with K=27\n 0:00:00.000 5M / 20M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 4\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 194) SPAdes started\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0\n 0:00:00.000 5M / 20M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 73) Converting paired reads\n 0:00:00.128 87M / 87M INFO General (binary_converter.cpp : 111) 7925 reads written\n 0:00:00.129 63M / 63M INFO General (read_converter.cpp : 81) Converting single reads\n 0:00:00.131 73M / 73M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.132 73M / 73M INFO General (read_converter.cpp : 87) Converting merged reads\n 0:00:00.134 73M / 73M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.174 25M / 29M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction\n 0:00:00.188 25M / 29M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.188 25M / 29M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.188 25M / 29M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting\n 0:00:00.189 25M / 29M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 4 threads. This might take a while.\n 0:00:00.190 25M / 29M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.190 25M / 29M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49994 Gb\n 0:00:00.190 25M / 29M INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304\n 0:00:00.412 42M / 57M INFO General (kmer_splitters.hpp : 293) Used 31700 reads\n 0:00:00.413 42M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:00.504 42M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 35249 kmers in total.\n 0:00:00.504 42M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:00.565 42M / 57M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction\n 0:00:00.566 42M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:00.567 42M / 57M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 4 threads. This might take a while.\n 0:00:00.567 42M / 57M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.568 42M / 57M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49992 Gb\n 0:00:00.568 42M / 57M INFO General (kmer_splitters.hpp : 97) Using cell size of 1048576\n 0:00:01.266 3G / 3G INFO General (kmer_splitters.hpp : 364) Processed 35249 kmers\n 0:00:01.266 3G / 3G INFO General (kmer_splitters.hpp : 369) Used 35249 kmers.\n 0:00:01.273 43M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:01.589 43M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 34510 kmers in total.\n 0:00:01.590 43M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:01.782 43M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:01.827 38M / 57M INFO General (kmer_index_builder.hpp : 150) Merging final buckets.\n 0:00:01.861 38M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 24880 bytes occupied (5.7676 bits per kmer).\n 0:00:01.862 38M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers\n 0:00:01.868 38M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.\n 0:00:01.869 38M / 57M INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping\n 0:00:01.870 38M / 57M INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K)\n 0:00:01.870 38M / 57M INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping\n 0:00:01.879 39M / 57M INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 404\n 0:00:01.879 39M / 57M INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 413\n 0:00:01.879 39M / 57M INFO Early tip clipping (early_simplification.hpp : 30) 7414 28-mers were removed by early tip clipper\n 0:00:01.880 39M / 57M INFO General (stage.cpp : 113) PROCEDURE == Condensing graph\n 0:00:01.883 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths\n 0:00:01.887 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2055 sequences extracted\n 0:00:01.890 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops\n 0:00:01.895 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected\n 0:00:01.897 37M / 57M INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)\n 0:00:01.897 37M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:01.898 37M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:01.912 38M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 18528 bytes occupied (4.20506 bits per kmer).\n 0:00:01.912 38M / 57M INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.001 38M / 57M INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM\n 0:00:02.004 38M / 57M INFO General (construction.cpp : 505) Processed 4110 edges\n 0:00:02.009 38M / 57M INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding\n 0:00:02.009 38M / 57M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7\n 0:00:02.010 38M / 57M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 695\n 0:00:02.010 38M / 57M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.010 38M / 57M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model\n 0:00:02.093 38M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2\n 0:00:02.301 38M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4\n 0:00:02.782 38M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8\n 0:00:03.348 38M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16\n 0:00:04.316 38M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32\n 0:00:04.316 38M / 57M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:04.318 38M / 57M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1\n 0:00:04.318 38M / 57M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 275\n 0:00:04.318 38M / 57M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 275\n 0:00:04.318 38M / 57M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 5132\n 0:00:04.319 38M / 57M INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 671.577\n 0:00:04.319 38M / 57M INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 275\n 0:00:04.319 38M / 57M INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0\n 0:00:04.319 38M / 57M INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification\n 0:00:04.319 38M / 57M INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning\n 0:00:04.319 38M / 57M INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled\n \n..\nry/000/99/working/spades_assembly/assembly/scaffolds.fasta\n * Paths in the assembly graph corresponding to the contigs are in /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/contigs.paths\n * Paths in the assembly graph corresponding to the scaffolds are in /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/scaffolds.paths\n * Assembly graph is in /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/assembly_graph.fastg\n * Assembly graph in GFA format is in /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa\n======= SPAdes pipeline finished WITH WARNINGS!\n=== Error correction and assembling warnings:\n * 0:00:06.824 33M / 103M WARN General (launcher.cpp : 172) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option.\n======= Warnings saved to /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/warnings.log\nSPAdes log can be found here: /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/spades.log\nThank you for using SPAdes!\n\nInsert size mean: 367.3 bp\nInsert size stdev: 37.3 bp\n\n\nCleaning k127 graph\nRepair multi way junctions (2023-10-24 14:37:50)\nFilter by read depth (2023-10-24 14:37:50)\nFilter homopolymer loops (2023-10-24 14:37:50)\nMerge all possible (2023-10-24 14:37:50)\nNormalise read depths (2023-10-24 14:37:50)\nRemove zero length segments (2023-10-24 14:37:50)\nSort link order (2023-10-24 14:37:50)\nGraph cleaning finished (2023-10-24 14:37:50)\nSaving /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2023-10-24 14:37:50)\nFilter by read depth (2023-10-24 14:37:50)\nFilter homopolymer loops (2023-10-24 14:37:50)\nMerge all possible (2023-10-24 14:37:50)\nNormalise read depths (2023-10-24 14:37:50)\nRemove zero length segments (2023-10-24 14:37:50)\nSort link order (2023-10-24 14:37:50)\nGraph cleaning finished (2023-10-24 14:37:50)\nSaving /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/k127_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2023-10-24 14:37:50)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 \n 47 \n 63 \n 77 \n 89 \n 99 \n 107 \n 115 \n 121 \n 127 1 1 5,513 5,513 5,513 0 5.00e-01 <-best\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/\n\n\nDetermining graph multiplicity (2023-10-24 14:37:51)\n Multiplicity is the number of times a sequence occurs in the underlying\nsequence. Single-copy contigs (those with a multiplicity of one, occurring only\nonce in the underlying sequence) are particularly useful.\n Multiplicity determination begins by identifying contigs which are clearly\nsingle-copy because they are of low depth and do not have more than one link\nper side.\n\nMedian depth of 10 longest contigs: 1.00\n\n\nInitial single copy segments:\n 1\n\n Unicycler now uses a greedy algorithm to propagate multiplicity through the\ngraph. For example, if two single-copy contigs merge together, the resulting\ncontig will get a multiplicity of two. When no more propagation is possible,\nadditional single-copy contigs are added and the process is repeated. This\nallows for multiplicity to be correctly assigned to the chromosome (at the\nmedian depth) but also for plasmids (which may be higher or lower in depth).\n\n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n FINDING NEW SINGLE-COPY \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \nREMOVING PROPAGATION TOLERANCE \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n\nSaving /galaxy/server/database/jobs_directory/000/99/working/001_best_spades_graph.gfa\n\n\nCleaning graph (2023-10-24 14:37:51)\n Unicycler now performs various cleaning procedures on the graph to remove\noverlaps and simplify the graph structure. The end result is a graph ready for\nbridging.\n\nGrouping graph edges based on overlap removal\n\r0 / 2 (0.0%)\r1 / 2 (50.0%)\r2 / 2 (100.0%)\n\nRemoving graph overlaps\n\n Bases Bases\n trimmed trimmed\n Segment from from\n number start end\n 1 63 64\nGraph overlaps removed\n\nSaving /galaxy/server/database/jobs_directory/000/99/working/002_overlaps_removed.gfa\n\n Unicycler now selects a set of anchor contigs from the single-copy contigs.\nThese are the contigs which will be connected via bridges to form the final\nassembly.\n\n\n1 anchor segments (5,386 bp) out of 1 total segments (5,386 bp)\n\nAnchor segments:\n 1\n\n\nCreating SPAdes contig bridges (2023-10-24 14:37:51)\n SPAdes uses paired-end information to perform repeat resolution (RR) and\nproduce contigs from the assembly graph. SPAdes saves the graph paths\ncorresponding to these contigs in the contigs.paths file. When one of these\npaths contains two or more anchor contigs, Unicycler can create a bridge from\nthe path.\n\nNo SPAdes contig bridges\n\n\nCreating loop unrolling bridges (2023-10-24 14:37:51)\n When a SPAdes contig path connects an anchor contig with the middle contig\nof a simple loop, Unicycler concludes that the sequences are contiguous (i.e.\nthe loop is not a separate piece of DNA). It then uses the read depth of the\nmiddle and repeat contigs to guess the number of times to traverse the loop and\nmakes a bridge.\n\nNo loop unrolling bridges made\nnone found\n\n\nLoading reads (2023-10-24 14:37:51)\n\r0 / 1 (0.0%)\r1 / 1 (100.0%) - 5,386 bp\r1 / 1 (100.0%) - 5,386 bp\n\n\nAssembling contigs and long reads with miniasm (2023-10-24 14:37:51)\n Unicycler uses miniasm to construct a string graph assembly using both the\nshort read contigs and the long reads. It will then use the resulting string\ngraph to produce bridges between contigs. This method requires decent coverage\nof long reads and therefore may not be fruitful if long reads are sparse.\nHowever, it does not rely on the short read assembly graph having good\nconnectivity and is able to bridge an assembly graph even when it contains many\ndead ends.\n Unicycler uses two types of \"reads\" as assembly input: anchor contigs from\nthe short-read assembly and actual long reads which overlap two or more of\nthese contigs. It then assembles them with miniasm.\n\nAligning long reads to graph using minimap\nSaving /galaxy/server/database/jobs_directory/000/99/working/miniasm_assembly/all_segments.fasta\n1\t5386\t3\t5081\t-\t1\t5386\t4\t5082\t5078\t5078\t255\tcm:i:1134\n1\t5386\t5090\t5383\t-\t1\t5386\t5088\t5381\t293\t293\t255\tcm:i:63\nNumber of minimap alignments: 1\n\nSaving to /galaxy/server/database/jobs_directory/000/99/working/miniasm_assembly/01_assembly_reads.fastq:\n 0 short-read contigs\n 1 long reads\n\nFinding overlaps with minimap... failed\nAssembling reads with miniasm... empty result\n\n\nCreating simple long read bridges (2023-10-24 14:37:51)\n Unicycler uses long read alignments (from minimap) to resolve simple repeat\nstructures in the graph. This takes care of some \"low-hanging fruit\" of the\ngraph simplification.\n\nAligning long reads to graph using minimap\nSaving /galaxy/server/database/jobs_directory/000/99/working/simple_bridging/all_segments.fasta\n1\t5386\t3\t5081\t-\t1\t5386\t4\t5082\t5078\t5078\t255\tcm:i:1134\n1\t5386\t5090\t5383\t-\t1\t5386\t5088\t5381\t293\t293\t255\tcm:i:63\nNumber of minimap alignments: 1\n\n Two-way junctions are defined as cases where two graph contigs (A and B)\njoin together (C) and then split apart again (D and E). This usually represents\na simple 2-copy repeat, and there are two possible options for its resolution:\n(A->C->D and B->C->E) or (A->C->E and B->C->D). Each read which spans such a\njunction gets to \"vote\" for option 1, option 2 or neither. Unicycler creates a\nbridge at each junction for the most voted for option.\n\nNo suitable two-way junctions present\n\n Simple loops are parts of the graph where two contigs (A and B) are\nconnected via a repeat (C) which loops back to itself (via D). It is possible\nto traverse the loop zero times (A->C->B), one time (A->C->D->C->B), two times\n(A->C->D->C->D->C->B), etc. Long reads which span the loop inform which is the\ncorrect number of times through. In this step, such reads are found and each is\naligned against alternative loop counts. A reads casts its \"vote\" for the loop\ncount it agrees best with, and Unicycler creates a bridge using the most voted\nfor count.\n\nNo suitable simple loops present\n\n\nDetermining low score threshold (2023-10-24 14:37:51)\n Before conducting semi-global alignment of the long reads to the assembly\ngraph, Unicycler must determine a minimum alignment score threshold such that\nnonsense alignments are excluded. To choose a threshold automatically, it\nexamines alignments between random sequences and selects a score a few standard\ndeviations above the mean.\n\nAutomatically choosing a threshold using random alignment scores.\n\nRandom alignment mean score: 61.66\n standard deviation: 1.31\n Low score threshold: 61.66 + (7 x 1.31) = 70.86\n\n\nAligning reads with minimap (2023-10-24 14:37:51)\n1\t5386\t5\t5077\t-\t1\t5386\t8\t5080\t5072\t5072\t255\tcm:i:945\n1\t5386\t5093\t5384\t-\t1\t5386\t5087\t5378\t291\t291\t255\tcm:i:52\n\nDone! 1 out of 1 reads aligned\n\n\nAligning reads (2023-10-24 14:37:51)\n1/1: 1 (5386 bp)\nminimap alignments:\n 5,5077,-,1,8,5080\n 5093,5384,-,1,5087,5378\nReference ranges:\n 1-: 0 - 5386\nRange: 1: 0 - 5386\n common 10-mers: 5464\n line 1: 5076 points, score=5074.000394 (good)\n line 2: 292 points, score=290.006826 (good)\nAll Seqan alignments (time to align = 0.040 s):\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 0 5085 0 5085 - 15255 100.00 100.00%\n 1 5085 5386 5085 5386 - 903 100.00 100.00%\nFinal alignments:\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 0 5085 0 5085 - 15255 100.00 100.00%\n 1 5085 5386 5085 5386 - 903 100.00 100.00%\n\n\nRead alignment summary (2023-10-24 14:37:51)\nTotal read count: 1\nFully aligned reads: 1\nPartially aligned reads: 0\nUnaligned reads: 0\nTotal bases aligned: 5,386 bp\nMean alignment identity: 100.0%\n\nDeleting /galaxy/server/database/jobs_directory/000/99/working/read_alignment/\n\nSetting the minimum scaled score to the 5.0th percentile of full read alignments: 0.00\n\n\nBuilding long read bridges (2023-10-24 14:37:51)\n Unicycler uses the long read alignments to produce bridges between anchor\nsegments. These bridges can be formed using as few as one long read, giving\nUnicycler the ability to bridge the graph even when long-read depth is low.\n\nMedian depth of 10 longest contigs: 1.00\n\n Consensus Consensus Target Search Path Best path Best path Best path Best path \n Start -> end Reads len (bp) time (s) len (bp) Search type time (s) count Best path len (bp) raw score scaled score length disc Quality\n\n\nApplying bridges (2023-10-24 14:37:51)\n Unicycler now applies to the graph in decreasing order of quality. This\nensures that when multiple, contradictory bridges exist, the most supported\noption is used.\n\nBridge type Start -> end Path Quality Result\n\nSaving /galaxy/server/database/jobs_directory/000/99/working/003_bridges_applied.gfa\n\n\nCleaning up leftover segments (2023-10-24 14:37:51)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2023-10-24 14:37:51)\n The assembly is now mostly finished and no more structural changes will be\nmade. Ideally the assembly graph should now have one contig per replicon and no\nerroneous contigs (i.e a complete assembly). If there are more contigs, then\nthe assembly is not complete.\n\nSaving /galaxy/server/database/jobs_directory/000/99/working/004_final_clean.gfa\n\nComponent Segments Links Length N50 Longest segment Status \n 1 1 1 5,386 5,386 5,386 complete\n\n\nPolishing assembly with Pilon (2023-10-24 14:37:51)\n Unicycler now conducts multiple rounds of Pilon in an attempt to repair any\nremaining small-scale errors with the assembly.\n\nAligning reads to find appropriate insert size range...\n bowtie2-build 0_insert_size_check.fasta 0_insert_size_check.fasta\n bowtie2 -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz -x 0_insert_size_check.fasta --fast --threads 4 -I 0 -X 5000 -S 0_alignments.sam\nInsert size 1st percentile: 263\nInsert size 99th percentile: 450\n\nPilon polish round 1\n bowtie2-build 1_polish_input.fasta 1_polish_input.fasta\n bowtie2 --local --very-sensitive-local --threads 4 -I 263 -X 450 -x 1_polish_input.fasta -S 1_paired_alignments.sam -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz\n samtools sort -@ 4 -o 1_paired_alignments.bam -O bam -T temp 1_paired_alignments.sam\n samtools index 1_paired_alignments.bam\n java -jar /usr/local/share/pilon-1.24-0/pilon.jar --genome 1_polish_input.fasta --changes --output 1_pilon --outdir /galaxy/server/database/jobs_directory/000/99/working/pilon_polish --fix bases --frags 1_paired_alignments.bam\nNo Pilon changes\n\nPilon polish round 2\n bowtie2-build 2_polish_input.fasta 2_polish_input.fasta\n bowtie2 --local --very-sensitive-local --threads 4 -I 263 -X 450 -x 2_polish_input.fasta -S 2_paired_alignments.sam -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz\n samtools sort -@ 4 -o 2_paired_alignments.bam -O bam -T temp 2_paired_alignments.sam\n samtools index 2_paired_alignments.bam\n java -jar /usr/local/share/pilon-1.24-0/pilon.jar --genome 2_polish_input.fasta --changes --output 2_pilon --outdir /galaxy/server/database/jobs_directory/000/99/working/pilon_polish --fix all --frags 2_paired_alignments.bam\nNo Pilon changes\n\nSaving /galaxy/server/database/jobs_directory/000/99/working/005_polished.gfa\n\n\nRotating completed replicons (2023-10-24 14:38:03)\n Any completed circular contigs (i.e. single contigs which have one link\nconnecting end to start) can have their start position changed without altering\nthe sequence. For consistency, Unicycler now searches for a starting gene (dnaA\nor repA) in each such contig, and if one is found, the contig is rotated to\nstart with that gene on the forward strand.\n\nSegment 1:\n makeblastdb -dbtype nucl -in replicon.fasta\n tblastn -db replicon.fasta -query /usr/local/lib/python3.9/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1\n\nSegment Length Depth Starting gene Position Strand Identity Coverage\n 1 5,386 1.00x none found \n\n\nAssembly complete (2023-10-24 14:38:13)\nSaving /galaxy/server/database/jobs_directory/000/99/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/99/working/assembly.fasta\n\n", "tool_stderr": "tput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\n", "job_stdout": "", "job_stderr": "", "stderr": "tput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\n", "stdout": "\nStarting Unicycler (2023-10-24 14:36:36)\n Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you\nprovided both short and long reads, Unicycler will perform a hybrid assembly.\nIt will first use SPAdes to make a short-read assembly graph, and then it will\nuse various methods to scaffold that graph with the long reads.\n For more information, please see https://github.com/rrwick/Unicycler\n\nCommand: /usr/local/bin/unicycler -t 4 -o ./ --verbosity 3 --pilon_path /usr/local/share/pilon-1.24-0/pilon.jar -1 fq1.fastq.gz -2 fq2.fastq.gz -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --no_correct --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2\n\nUnicycler version: v0.4.8\nUsing 4 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/99/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 3.14.1 good /usr/local/bin/spades.py \n racon 1.4.20 good /usr/local/bin/racon \n makeblastdb 2.12.0+ good /usr/local/bin/makeblastdb \n tblastn 2.12.0+ good /usr/local/bin/tblastn \n bowtie2-build 2.4.4 good /usr/local/bin/bowtie2-build \n bowtie2 2.4.4 good /usr/local/bin/bowtie2 \n samtools 1.14 good /usr/local/bin/samtools \n java 11.0.9.1-internal good /usr/local/bin/java \n pilon 1.24 good /usr/local/share/pilon-1.24-0/pilon.jar\n bcftools not used \n\n\nChoosing k-mer range for assembly (2023-10-24 14:36:38)\n Unicycler chooses a k-mer range for SPAdes based on the length of the input\nreads. It uses a wide range of many k-mer sizes to maximise the chance of\nfinding an ideal assembly.\n\nSPAdes maximum k-mer: 127\nMedian read length: 251\nK-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127\n\n\nSPAdes assemblies (2023-10-24 14:36:38)\n Unicycler now uses SPAdes to assemble the short reads. It scores the\nassembly graph for each k-mer using the number of contigs (fewer is better) and\nthe number of dead ends (fewer is better). The score function is 1/(c*(d+2)),\nwhere c is the contig count and d is the dead end count.\n\n== Warning == No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly -k 27,47,63,77,89,99,107,115,121,127 --threads 4 --only-assembler -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz\n\nSystem information:\n SPAdes version: 3.14.1\n Python version: 3.9.9\n OS: Linux-5.10.176+-x86_64-with-glibc2.28\nOutput dir: /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Standard mode\n For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz']\n right reads: ['/galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27, 47, 63, 77, 89, 99, 107, 115, 121, 127]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/tmp\n Threads: 4\n Memory limit (in Gb): 78\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/spades.log\n/galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz: max reads length: 251\n/galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz: max reads length: 251\nReads length: 251\n===== Before start started.\n===== Assembling started.\n===== K27 started.\n== Running: /usr/local/bin/spades-core /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/K27/configs/config.info\nWARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is tmp_contigs.fasta\n 0:00:00.000 5M / 20M INFO General (main.cpp : 75) Loaded config from /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/K27/configs/config.info\n 0:00:00.000 5M / 20M INFO General (memory_limit.cpp : 49) Memory limit set to 78 Gb\n 0:00:00.000 5M / 20M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 5M / 20M INFO General (main.cpp : 86) Maximum k-mer length: 128\n 0:00:00.000 5M / 20M INFO General (main.cpp : 87) Assembling dataset (/galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/dataset.info) with K=27\n 0:00:00.000 5M / 20M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 4\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 194) SPAdes started\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0\n 0:00:00.000 5M / 20M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 73) Converting paired reads\n 0:00:00.128 87M / 87M INFO General (binary_converter.cpp : 111) 7925 reads written\n 0:00:00.129 63M / 63M INFO General (read_converter.cpp : 81) Converting single reads\n 0:00:00.131 73M / 73M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.132 73M / 73M INFO General (read_converter.cpp : 87) Converting merged reads\n 0:00:00.134 73M / 73M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.174 25M / 29M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction\n 0:00:00.188 25M / 29M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.188 25M / 29M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.188 25M / 29M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting\n 0:00:00.189 25M / 29M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 4 threads. This might take a while.\n 0:00:00.190 25M / 29M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.190 25M / 29M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49994 Gb\n 0:00:00.190 25M / 29M INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304\n 0:00:00.412 42M / 57M INFO General (kmer_splitters.hpp : 293) Used 31700 reads\n 0:00:00.413 42M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:00.504 42M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 35249 kmers in total.\n 0:00:00.504 42M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:00.565 42M / 57M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction\n 0:00:00.566 42M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:00.567 42M / 57M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 4 threads. This might take a while.\n 0:00:00.567 42M / 57M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.568 42M / 57M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49992 Gb\n 0:00:00.568 42M / 57M INFO General (kmer_splitters.hpp : 97) Using cell size of 1048576\n 0:00:01.266 3G / 3G INFO General (kmer_splitters.hpp : 364) Processed 35249 kmers\n 0:00:01.266 3G / 3G INFO General (kmer_splitters.hpp : 369) Used 35249 kmers.\n 0:00:01.273 43M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:01.589 43M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 34510 kmers in total.\n 0:00:01.590 43M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:01.782 43M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:01.827 38M / 57M INFO General (kmer_index_builder.hpp : 150) Merging final buckets.\n 0:00:01.861 38M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 24880 bytes occupied (5.7676 bits per kmer).\n 0:00:01.862 38M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers\n 0:00:01.868 38M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.\n 0:00:01.869 38M / 57M INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping\n 0:00:01.870 38M / 57M INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K)\n 0:00:01.870 38M / 57M INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping\n 0:00:01.879 39M / 57M INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 404\n 0:00:01.879 39M / 57M INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 413\n 0:00:01.879 39M / 57M INFO Early tip clipping (early_simplification.hpp : 30) 7414 28-mers were removed by early tip clipper\n 0:00:01.880 39M / 57M INFO General (stage.cpp : 113) PROCEDURE == Condensing graph\n 0:00:01.883 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths\n 0:00:01.887 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2055 sequences extracted\n 0:00:01.890 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops\n 0:00:01.895 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected\n 0:00:01.897 37M / 57M INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)\n 0:00:01.897 37M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:01.898 37M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:01.912 38M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 18528 bytes occupied (4.20506 bits per kmer).\n 0:00:01.912 38M / 57M INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.001 38M / 57M INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM\n 0:00:02.004 38M / 57M INFO General (construction.cpp : 505) Processed 4110 edges\n 0:00:02.009 38M / 57M INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding\n 0:00:02.009 38M / 57M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7\n 0:00:02.010 38M / 57M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 695\n 0:00:02.010 38M / 57M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.010 38M / 57M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model\n 0:00:02.093 38M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2\n 0:00:02.301 38M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4\n 0:00:02.782 38M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8\n 0:00:03.348 38M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16\n 0:00:04.316 38M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32\n 0:00:04.316 38M / 57M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:04.318 38M / 57M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1\n 0:00:04.318 38M / 57M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 275\n 0:00:04.318 38M / 57M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 275\n 0:00:04.318 38M / 57M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 5132\n 0:00:04.319 38M / 57M INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 671.577\n 0:00:04.319 38M / 57M INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 275\n 0:00:04.319 38M / 57M INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0\n 0:00:04.319 38M / 57M INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification\n 0:00:04.319 38M / 57M INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning\n 0:00:04.319 38M / 57M INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled\n \n..\nry/000/99/working/spades_assembly/assembly/scaffolds.fasta\n * Paths in the assembly graph corresponding to the contigs are in /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/contigs.paths\n * Paths in the assembly graph corresponding to the scaffolds are in /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/scaffolds.paths\n * Assembly graph is in /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/assembly_graph.fastg\n * Assembly graph in GFA format is in /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa\n======= SPAdes pipeline finished WITH WARNINGS!\n=== Error correction and assembling warnings:\n * 0:00:06.824 33M / 103M WARN General (launcher.cpp : 172) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option.\n======= Warnings saved to /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/warnings.log\nSPAdes log can be found here: /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/assembly/spades.log\nThank you for using SPAdes!\n\nInsert size mean: 367.3 bp\nInsert size stdev: 37.3 bp\n\n\nCleaning k127 graph\nRepair multi way junctions (2023-10-24 14:37:50)\nFilter by read depth (2023-10-24 14:37:50)\nFilter homopolymer loops (2023-10-24 14:37:50)\nMerge all possible (2023-10-24 14:37:50)\nNormalise read depths (2023-10-24 14:37:50)\nRemove zero length segments (2023-10-24 14:37:50)\nSort link order (2023-10-24 14:37:50)\nGraph cleaning finished (2023-10-24 14:37:50)\nSaving /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2023-10-24 14:37:50)\nFilter by read depth (2023-10-24 14:37:50)\nFilter homopolymer loops (2023-10-24 14:37:50)\nMerge all possible (2023-10-24 14:37:50)\nNormalise read depths (2023-10-24 14:37:50)\nRemove zero length segments (2023-10-24 14:37:50)\nSort link order (2023-10-24 14:37:50)\nGraph cleaning finished (2023-10-24 14:37:50)\nSaving /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/k127_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2023-10-24 14:37:50)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 \n 47 \n 63 \n 77 \n 89 \n 99 \n 107 \n 115 \n 121 \n 127 1 1 5,513 5,513 5,513 0 5.00e-01 <-best\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/99/working/spades_assembly/\n\n\nDetermining graph multiplicity (2023-10-24 14:37:51)\n Multiplicity is the number of times a sequence occurs in the underlying\nsequence. Single-copy contigs (those with a multiplicity of one, occurring only\nonce in the underlying sequence) are particularly useful.\n Multiplicity determination begins by identifying contigs which are clearly\nsingle-copy because they are of low depth and do not have more than one link\nper side.\n\nMedian depth of 10 longest contigs: 1.00\n\n\nInitial single copy segments:\n 1\n\n Unicycler now uses a greedy algorithm to propagate multiplicity through the\ngraph. For example, if two single-copy contigs merge together, the resulting\ncontig will get a multiplicity of two. When no more propagation is possible,\nadditional single-copy contigs are added and the process is repeated. This\nallows for multiplicity to be correctly assigned to the chromosome (at the\nmedian depth) but also for plasmids (which may be higher or lower in depth).\n\n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n FINDING NEW SINGLE-COPY \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \nREMOVING PROPAGATION TOLERANCE \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n\nSaving /galaxy/server/database/jobs_directory/000/99/working/001_best_spades_graph.gfa\n\n\nCleaning graph (2023-10-24 14:37:51)\n Unicycler now performs various cleaning procedures on the graph to remove\noverlaps and simplify the graph structure. The end result is a graph ready for\nbridging.\n\nGrouping graph edges based on overlap removal\n\r0 / 2 (0.0%)\r1 / 2 (50.0%)\r2 / 2 (100.0%)\n\nRemoving graph overlaps\n\n Bases Bases\n trimmed trimmed\n Segment from from\n number start end\n 1 63 64\nGraph overlaps removed\n\nSaving /galaxy/server/database/jobs_directory/000/99/working/002_overlaps_removed.gfa\n\n Unicycler now selects a set of anchor contigs from the single-copy contigs.\nThese are the contigs which will be connected via bridges to form the final\nassembly.\n\n\n1 anchor segments (5,386 bp) out of 1 total segments (5,386 bp)\n\nAnchor segments:\n 1\n\n\nCreating SPAdes contig bridges (2023-10-24 14:37:51)\n SPAdes uses paired-end information to perform repeat resolution (RR) and\nproduce contigs from the assembly graph. SPAdes saves the graph paths\ncorresponding to these contigs in the contigs.paths file. When one of these\npaths contains two or more anchor contigs, Unicycler can create a bridge from\nthe path.\n\nNo SPAdes contig bridges\n\n\nCreating loop unrolling bridges (2023-10-24 14:37:51)\n When a SPAdes contig path connects an anchor contig with the middle contig\nof a simple loop, Unicycler concludes that the sequences are contiguous (i.e.\nthe loop is not a separate piece of DNA). It then uses the read depth of the\nmiddle and repeat contigs to guess the number of times to traverse the loop and\nmakes a bridge.\n\nNo loop unrolling bridges made\nnone found\n\n\nLoading reads (2023-10-24 14:37:51)\n\r0 / 1 (0.0%)\r1 / 1 (100.0%) - 5,386 bp\r1 / 1 (100.0%) - 5,386 bp\n\n\nAssembling contigs and long reads with miniasm (2023-10-24 14:37:51)\n Unicycler uses miniasm to construct a string graph assembly using both the\nshort read contigs and the long reads. It will then use the resulting string\ngraph to produce bridges between contigs. This method requires decent coverage\nof long reads and therefore may not be fruitful if long reads are sparse.\nHowever, it does not rely on the short read assembly graph having good\nconnectivity and is able to bridge an assembly graph even when it contains many\ndead ends.\n Unicycler uses two types of \"reads\" as assembly input: anchor contigs from\nthe short-read assembly and actual long reads which overlap two or more of\nthese contigs. It then assembles them with miniasm.\n\nAligning long reads to graph using minimap\nSaving /galaxy/server/database/jobs_directory/000/99/working/miniasm_assembly/all_segments.fasta\n1\t5386\t3\t5081\t-\t1\t5386\t4\t5082\t5078\t5078\t255\tcm:i:1134\n1\t5386\t5090\t5383\t-\t1\t5386\t5088\t5381\t293\t293\t255\tcm:i:63\nNumber of minimap alignments: 1\n\nSaving to /galaxy/server/database/jobs_directory/000/99/working/miniasm_assembly/01_assembly_reads.fastq:\n 0 short-read contigs\n 1 long reads\n\nFinding overlaps with minimap... failed\nAssembling reads with miniasm... empty result\n\n\nCreating simple long read bridges (2023-10-24 14:37:51)\n Unicycler uses long read alignments (from minimap) to resolve simple repeat\nstructures in the graph. This takes care of some \"low-hanging fruit\" of the\ngraph simplification.\n\nAligning long reads to graph using minimap\nSaving /galaxy/server/database/jobs_directory/000/99/working/simple_bridging/all_segments.fasta\n1\t5386\t3\t5081\t-\t1\t5386\t4\t5082\t5078\t5078\t255\tcm:i:1134\n1\t5386\t5090\t5383\t-\t1\t5386\t5088\t5381\t293\t293\t255\tcm:i:63\nNumber of minimap alignments: 1\n\n Two-way junctions are defined as cases where two graph contigs (A and B)\njoin together (C) and then split apart again (D and E). This usually represents\na simple 2-copy repeat, and there are two possible options for its resolution:\n(A->C->D and B->C->E) or (A->C->E and B->C->D). Each read which spans such a\njunction gets to \"vote\" for option 1, option 2 or neither. Unicycler creates a\nbridge at each junction for the most voted for option.\n\nNo suitable two-way junctions present\n\n Simple loops are parts of the graph where two contigs (A and B) are\nconnected via a repeat (C) which loops back to itself (via D). It is possible\nto traverse the loop zero times (A->C->B), one time (A->C->D->C->B), two times\n(A->C->D->C->D->C->B), etc. Long reads which span the loop inform which is the\ncorrect number of times through. In this step, such reads are found and each is\naligned against alternative loop counts. A reads casts its \"vote\" for the loop\ncount it agrees best with, and Unicycler creates a bridge using the most voted\nfor count.\n\nNo suitable simple loops present\n\n\nDetermining low score threshold (2023-10-24 14:37:51)\n Before conducting semi-global alignment of the long reads to the assembly\ngraph, Unicycler must determine a minimum alignment score threshold such that\nnonsense alignments are excluded. To choose a threshold automatically, it\nexamines alignments between random sequences and selects a score a few standard\ndeviations above the mean.\n\nAutomatically choosing a threshold using random alignment scores.\n\nRandom alignment mean score: 61.66\n standard deviation: 1.31\n Low score threshold: 61.66 + (7 x 1.31) = 70.86\n\n\nAligning reads with minimap (2023-10-24 14:37:51)\n1\t5386\t5\t5077\t-\t1\t5386\t8\t5080\t5072\t5072\t255\tcm:i:945\n1\t5386\t5093\t5384\t-\t1\t5386\t5087\t5378\t291\t291\t255\tcm:i:52\n\nDone! 1 out of 1 reads aligned\n\n\nAligning reads (2023-10-24 14:37:51)\n1/1: 1 (5386 bp)\nminimap alignments:\n 5,5077,-,1,8,5080\n 5093,5384,-,1,5087,5378\nReference ranges:\n 1-: 0 - 5386\nRange: 1: 0 - 5386\n common 10-mers: 5464\n line 1: 5076 points, score=5074.000394 (good)\n line 2: 292 points, score=290.006826 (good)\nAll Seqan alignments (time to align = 0.040 s):\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 0 5085 0 5085 - 15255 100.00 100.00%\n 1 5085 5386 5085 5386 - 903 100.00 100.00%\nFinal alignments:\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 0 5085 0 5085 - 15255 100.00 100.00%\n 1 5085 5386 5085 5386 - 903 100.00 100.00%\n\n\nRead alignment summary (2023-10-24 14:37:51)\nTotal read count: 1\nFully aligned reads: 1\nPartially aligned reads: 0\nUnaligned reads: 0\nTotal bases aligned: 5,386 bp\nMean alignment identity: 100.0%\n\nDeleting /galaxy/server/database/jobs_directory/000/99/working/read_alignment/\n\nSetting the minimum scaled score to the 5.0th percentile of full read alignments: 0.00\n\n\nBuilding long read bridges (2023-10-24 14:37:51)\n Unicycler uses the long read alignments to produce bridges between anchor\nsegments. These bridges can be formed using as few as one long read, giving\nUnicycler the ability to bridge the graph even when long-read depth is low.\n\nMedian depth of 10 longest contigs: 1.00\n\n Consensus Consensus Target Search Path Best path Best path Best path Best path \n Start -> end Reads len (bp) time (s) len (bp) Search type time (s) count Best path len (bp) raw score scaled score length disc Quality\n\n\nApplying bridges (2023-10-24 14:37:51)\n Unicycler now applies to the graph in decreasing order of quality. This\nensures that when multiple, contradictory bridges exist, the most supported\noption is used.\n\nBridge type Start -> end Path Quality Result\n\nSaving /galaxy/server/database/jobs_directory/000/99/working/003_bridges_applied.gfa\n\n\nCleaning up leftover segments (2023-10-24 14:37:51)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2023-10-24 14:37:51)\n The assembly is now mostly finished and no more structural changes will be\nmade. Ideally the assembly graph should now have one contig per replicon and no\nerroneous contigs (i.e a complete assembly). If there are more contigs, then\nthe assembly is not complete.\n\nSaving /galaxy/server/database/jobs_directory/000/99/working/004_final_clean.gfa\n\nComponent Segments Links Length N50 Longest segment Status \n 1 1 1 5,386 5,386 5,386 complete\n\n\nPolishing assembly with Pilon (2023-10-24 14:37:51)\n Unicycler now conducts multiple rounds of Pilon in an attempt to repair any\nremaining small-scale errors with the assembly.\n\nAligning reads to find appropriate insert size range...\n bowtie2-build 0_insert_size_check.fasta 0_insert_size_check.fasta\n bowtie2 -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz -x 0_insert_size_check.fasta --fast --threads 4 -I 0 -X 5000 -S 0_alignments.sam\nInsert size 1st percentile: 263\nInsert size 99th percentile: 450\n\nPilon polish round 1\n bowtie2-build 1_polish_input.fasta 1_polish_input.fasta\n bowtie2 --local --very-sensitive-local --threads 4 -I 263 -X 450 -x 1_polish_input.fasta -S 1_paired_alignments.sam -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz\n samtools sort -@ 4 -o 1_paired_alignments.bam -O bam -T temp 1_paired_alignments.sam\n samtools index 1_paired_alignments.bam\n java -jar /usr/local/share/pilon-1.24-0/pilon.jar --genome 1_polish_input.fasta --changes --output 1_pilon --outdir /galaxy/server/database/jobs_directory/000/99/working/pilon_polish --fix bases --frags 1_paired_alignments.bam\nNo Pilon changes\n\nPilon polish round 2\n bowtie2-build 2_polish_input.fasta 2_polish_input.fasta\n bowtie2 --local --very-sensitive-local --threads 4 -I 263 -X 450 -x 2_polish_input.fasta -S 2_paired_alignments.sam -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz\n samtools sort -@ 4 -o 2_paired_alignments.bam -O bam -T temp 2_paired_alignments.sam\n samtools index 2_paired_alignments.bam\n java -jar /usr/local/share/pilon-1.24-0/pilon.jar --genome 2_polish_input.fasta --changes --output 2_pilon --outdir /galaxy/server/database/jobs_directory/000/99/working/pilon_polish --fix all --frags 2_paired_alignments.bam\nNo Pilon changes\n\nSaving /galaxy/server/database/jobs_directory/000/99/working/005_polished.gfa\n\n\nRotating completed replicons (2023-10-24 14:38:03)\n Any completed circular contigs (i.e. single contigs which have one link\nconnecting end to start) can have their start position changed without altering\nthe sequence. For consistency, Unicycler now searches for a starting gene (dnaA\nor repA) in each such contig, and if one is found, the contig is rotated to\nstart with that gene on the forward strand.\n\nSegment 1:\n makeblastdb -dbtype nucl -in replicon.fasta\n tblastn -db replicon.fasta -query /usr/local/lib/python3.9/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1\n\nSegment Length Depth Starting gene Position Strand Identity Coverage\n 1 5,386 1.00x none found \n\n\nAssembly complete (2023-10-24 14:38:13)\nSaving /galaxy/server/database/jobs_directory/000/99/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/99/working/assembly.fasta\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "97.0000000"}, {"title": "Job End Time", "value": "2023-10-24 14:38:13", "plugin": "core", "name": "end_epoch", "raw_value": "1698158293.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:36:36", "plugin": "core", "name": "start_epoch", "raw_value": "1698158196.0000000"}, {"title": "Memory Allocated (MB)", "value": "40000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "40000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "unicycler/0.4.8.0-2", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.4.8.0", "test_index": 2, "time_seconds": 224.6271412372589, "inputs": {"paired_unpaired|fastq_input1": {"src": "hdca", "id": "d8c45a6ea5797d07"}, "paired_unpaired|fastq_input_selector": "paired_collection", "mode": "normal", "min_fasta_length": "100", "linear_seqs": "0", "spades|no_correct": true, "spades|min_kmer_frac": "0.2", "spades|max_kmer_frac": "0.95", "spades|kmer_count": "10", "spades|depth_filter": "0.25", "rotation|no_rotate": false, "rotation|start_gene_id": "90", "rotation|start_gene_cov": "95", "pilon|no_pilon": true, "pilon|min_polish_size": "1000", "graph_clean|min_component_size": "1000", "graph_clean|min_dead_end_size": "1000", "lr_align|scores": "3,-6,-5,-2"}, "job": {"model_class": "Job", "id": "0193434d2ad8346d", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:42:08.480255", "create_time": "2023-10-24T14:38:37.701306", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0", "history_id": "639c57257ba4f009", "external_id": "gxy-hcnnm", "command_line": "ln -s '/galaxy/server/database/objects/6/0/3/dataset_6037a213-0b9f-44d4-9a2f-c0d5f2c08581.dat' fq1.fastq && ln -s '/galaxy/server/database/objects/7/6/f/dataset_76f88e84-c080-448a-810f-14b7e2e43e09.dat' fq2.fastq && pilon=`pilon --jar_dir` && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 --pilon_path $pilon -1 'fq1.fastq' -2 'fq2.fastq' --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --no_correct --min_kmer_frac '0.2' --max_kmer_frac '0.95' --kmer_count '10' --depth_filter '0.25' --start_gene_id '90.0' --start_gene_cov '95.0' --no_pilon --min_polish_size '1000' --min_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"scores\": \"3,-6,-5,-2\"}", "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", "pilon": "{\"min_polish_size\": \"1000\", \"no_pilon\": \"true\"}", "rotation": "{\"no_rotate\": \"false\", \"start_gene_cov\": \"95.0\", \"start_gene_id\": \"90.0\", \"start_genes\": null}", "spades": "{\"depth_filter\": \"0.25\", \"kmer_count\": \"10\", \"kmers\": \"\", \"largest_component\": \"false\", \"max_kmer_frac\": \"0.95\", \"min_kmer_frac\": \"0.2\", \"no_correct\": \"true\"}", "min_anchor_seg_len": "\"\"", "linear_seqs": "\"0\"", "min_fasta_length": "\"100\"", "mode": "\"normal\"", "long": null, "paired_unpaired": "{\"__current_case__\": 1, \"fastq_input1\": {\"values\": [{\"id\": 20, \"src\": \"hdca\"}]}, \"fastq_input_selector\": \"paired_collection\"}"}, "inputs": {"fastq_input11": {"id": "82e8ff759cb4347c", "src": "hda", "uuid": "6037a213-0b9f-44d4-9a2f-c0d5f2c08581"}, "fastq_input12": {"id": "82f4a631611ce5e2", "src": "hda", "uuid": "76f88e84-c080-448a-810f-14b7e2e43e09"}}, "outputs": {"assembly_graph": {"id": "a536e486e3bf0b12", "src": "hda", "uuid": "063c1622-8862-4bf3-9a07-3d303d34e758"}, "assembly": {"id": "19c3993913d7afef", "src": "hda", "uuid": "996993d2-92bc-47d5-9382-79f4ddb9a155"}}, "output_collections": {}, "tool_stdout": "\nStarting Unicycler (2023-10-24 14:40:34)\n Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you\nprovided only short reads, Unicycler will essentially function as a SPAdes-\noptimiser. It will try many k-mer sizes, choose the best based on contig length\nand graph connectivity, and scaffold the graph using SPAdes repeat resolution.\n For more information, please see https://github.com/rrwick/Unicycler\n\nCommand: /usr/local/bin/unicycler -t 4 -o ./ --verbosity 3 --pilon_path /usr/local/share/pilon-1.24-0/pilon.jar -1 fq1.fastq -2 fq2.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --no_correct --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --no_pilon --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2\n\nUnicycler version: v0.4.8\nUsing 4 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/102/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 3.14.1 good /usr/local/bin/spades.py \n racon not used \n makeblastdb 2.12.0+ good /usr/local/bin/makeblastdb\n tblastn 2.12.0+ good /usr/local/bin/tblastn \n bowtie2-build not used \n bowtie2 not used \n samtools not used \n java not used \n pilon not used \n bcftools not used \n\n\nChoosing k-mer range for assembly (2023-10-24 14:40:36)\n Unicycler chooses a k-mer range for SPAdes based on the length of the input\nreads. It uses a wide range of many k-mer sizes to maximise the chance of\nfinding an ideal assembly.\n\nSPAdes maximum k-mer: 127\nMedian read length: 251\nK-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127\n\n\nSPAdes assemblies (2023-10-24 14:40:36)\n Unicycler now uses SPAdes to assemble the short reads. It scores the\nassembly graph for each k-mer using the number of contigs (fewer is better) and\nthe number of dead ends (fewer is better). The score function is 1/(c*(d+2)),\nwhere c is the contig count and d is the dead end count.\n\n== Warning == No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly -k 27,47,63,77,89,99,107,115,121,127 --threads 4 --only-assembler -1 /galaxy/server/database/jobs_directory/000/102/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/102/working/fq2.fastq\n\nSystem information:\n SPAdes version: 3.14.1\n Python version: 3.9.9\n OS: Linux-5.10.176+-x86_64-with-glibc2.28\nOutput dir: /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Standard mode\n For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/102/working/fq1.fastq']\n right reads: ['/galaxy/server/database/jobs_directory/000/102/working/fq2.fastq']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27, 47, 63, 77, 89, 99, 107, 115, 121, 127]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/tmp\n Threads: 4\n Memory limit (in Gb): 78\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/spades.log\n/galaxy/server/database/jobs_directory/000/102/working/fq1.fastq: max reads length: 251\n/galaxy/server/database/jobs_directory/000/102/working/fq2.fastq: max reads length: 251\nReads length: 251\n===== Before start started.\n===== Assembling started.\n===== K27 started.\n== Running: /usr/local/bin/spades-core /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K27/configs/config.info\nWARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is tmp_contigs.fasta\n 0:00:00.000 5M / 20M INFO General (main.cpp : 75) Loaded config from /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K27/configs/config.info\n 0:00:00.000 5M / 20M INFO General (memory_limit.cpp : 49) Memory limit set to 78 Gb\n 0:00:00.000 5M / 20M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 5M / 20M INFO General (main.cpp : 86) Maximum k-mer length: 128\n 0:00:00.000 5M / 20M INFO General (main.cpp : 87) Assembling dataset (/galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/dataset.info) with K=27\n 0:00:00.000 5M / 20M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 4\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 194) SPAdes started\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0\n 0:00:00.000 5M / 20M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 73) Converting paired reads\n 0:00:00.107 87M / 87M INFO General (binary_converter.cpp : 111) 7925 reads written\n 0:00:00.108 63M / 63M INFO General (read_converter.cpp : 81) Converting single reads\n 0:00:00.110 73M / 73M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.110 73M / 73M INFO General (read_converter.cpp : 87) Converting merged reads\n 0:00:00.111 73M / 73M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.152 25M / 29M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction\n 0:00:00.164 25M / 29M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.164 25M / 29M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.164 25M / 29M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting\n 0:00:00.165 25M / 29M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 4 threads. This might take a while.\n 0:00:00.166 25M / 29M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.166 25M / 29M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49995 Gb\n 0:00:00.166 25M / 29M INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304\n 0:00:00.404 42M / 57M INFO General (kmer_splitters.hpp : 293) Used 31700 reads\n 0:00:00.405 42M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:00.487 42M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 35249 kmers in total.\n 0:00:00.488 42M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:00.544 42M / 57M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction\n 0:00:00.545 42M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:00.545 42M / 57M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 4 threads. This might take a while.\n 0:00:00.546 42M / 57M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.546 42M / 57M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49992 Gb\n 0:00:00.546 42M / 57M INFO General (kmer_splitters.hpp : 97) Using cell size of 1048576\n 0:00:01.258 3G / 3G INFO General (kmer_splitters.hpp : 364) Processed 35249 kmers\n 0:00:01.258 3G / 3G INFO General (kmer_splitters.hpp : 369) Used 35249 kmers.\n 0:00:01.267 43M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:01.615 43M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 34510 kmers in total.\n 0:00:01.616 43M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:01.829 43M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:01.876 39M / 57M INFO General (kmer_index_builder.hpp : 150) Merging final buckets.\n 0:00:01.910 39M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 24880 bytes occupied (5.7676 bits per kmer).\n 0:00:01.910 39M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers\n 0:00:01.916 39M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.\n 0:00:01.917 39M / 57M INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping\n 0:00:01.918 39M / 57M INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K)\n 0:00:01.918 39M / 57M INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping\n 0:00:01.927 39M / 57M INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 404\n 0:00:01.927 39M / 57M INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 413\n 0:00:01.928 39M / 57M INFO Early tip clipping (early_simplification.hpp : 30) 7414 28-mers were removed by early tip clipper\n 0:00:01.928 39M / 57M INFO General (stage.cpp : 113) PROCEDURE == Condensing graph\n 0:00:01.932 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths\n 0:00:01.937 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2055 sequences extracted\n 0:00:01.940 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops\n 0:00:01.945 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected\n 0:00:01.948 39M / 57M INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)\n 0:00:01.948 39M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:01.948 39M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:01.967 40M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 18528 bytes occupied (4.20506 bits per kmer).\n 0:00:01.967 40M / 57M INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.059 40M / 57M INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM\n 0:00:02.061 40M / 57M INFO General (construction.cpp : 505) Processed 4110 edges\n 0:00:02.068 40M / 57M INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding\n 0:00:02.068 40M / 57M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7\n 0:00:02.069 40M / 57M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 695\n 0:00:02.069 40M / 57M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.069 40M / 57M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model\n 0:00:02.151 40M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2\n 0:00:02.362 40M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4\n 0:00:02.848 40M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8\n 0:00:03.411 40M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16\n 0:00:04.377 40M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32\n 0:00:04.377 40M / 57M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:04.379 40M / 57M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1\n 0:00:04.379 40M / 57M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 275\n 0:00:04.379 40M / 57M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 275\n 0:00:04.379 40M / 57M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 5132\n 0:00:04.379 40M / 57M INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 671.577\n 0:00:04.379 40M / 57M INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 275\n 0:00:04.380 40M / 57M INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0\n 0:00:04.380 40M / 57M INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification\n 0:00:04.380 40M / 57M INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning\n 0:00:04.380 40M / 57M INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled\n 0:00:04.380 40M / 57M INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover\n 0:00:04.381 40M / 57M INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge r\n..\n overlaps\n 0:00:06.613 33M / 102M INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps\n 0:00:06.613 33M / 102M INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps\n 0:00:06.613 33M / 102M INFO PEResolver (pe_resolver.hpp : 308) Splitting paths\n 0:00:06.613 33M / 102M INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths\n 0:00:06.614 33M / 102M INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 267) Paths finalized\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 439) Closing gaps in paths\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 467) Gap closing completed\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 296) Traversing tandem repeats\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 306) Traversed 0 loops\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 244) Finalizing paths\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 246) Deduplicating paths\n 0:00:06.615 33M / 102M INFO General (launcher.cpp : 250) Paths deduplicated\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 298) Sorting paths\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps\n 0:00:06.615 33M / 102M INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps\n 0:00:06.615 33M / 102M INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 308) Splitting paths\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed\n 0:00:06.615 33M / 102M INFO General (launcher.cpp : 267) Paths finalized\n 0:00:06.616 33M / 102M INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished\n 0:00:06.616 31M / 102M INFO StageManager (stage.cpp : 166) STAGE == Contig Output\n 0:00:06.616 31M / 102M INFO General (contig_output.hpp : 21) Outputting contigs to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/before_rr.fasta\n 0:00:06.624 31M / 102M INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/assembly_graph_with_scaffolds.gfa\n 0:00:06.625 31M / 102M INFO General (contig_output_stage.cpp : 160) Outputting FastG graph to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/assembly_graph.fastg\n 0:00:06.632 31M / 102M INFO General (contig_output_stage.cpp : 190) Breaking scaffolds\n 0:00:06.633 31M / 102M INFO General (contig_output_stage.cpp : 95) Outputting contigs to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/final_contigs.fasta\n 0:00:06.638 31M / 102M INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/final_contigs.paths\n 0:00:06.645 31M / 102M INFO General (contig_output_stage.cpp : 95) Outputting contigs to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/scaffolds.fasta\n 0:00:06.652 31M / 102M INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/scaffolds.paths\n 0:00:06.658 31M / 102M INFO General (contig_output_stage.cpp : 108) Populating GFA with scaffold paths\n 0:00:06.669 31M / 102M INFO General (pipeline.cpp : 259) SPAdes finished\n 0:00:06.674 31M / 102M INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 6 seconds\n===== K127 finished.\n===== Copy files started.\n== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/before_rr.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/before_rr.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/final_contigs.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/contigs.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/strain_graph.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/strain_graph.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/scaffolds.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/scaffolds.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/scaffolds.paths /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/scaffolds.paths /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/final_contigs.paths /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/contigs.paths\n===== Copy files finished.\n===== Assembling finished.\n===== Breaking scaffolds started.\n== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/scaffolds.fasta --misc_dir /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/misc --threshold_for_breaking_scaffolds 3\n===== Breaking scaffolds finished.\n===== Terminate started.\n===== Terminate finished.\n * Assembled contigs are in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/contigs.fasta\n * Assembled scaffolds are in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/scaffolds.fasta\n * Paths in the assembly graph corresponding to the contigs are in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/contigs.paths\n * Paths in the assembly graph corresponding to the scaffolds are in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/scaffolds.paths\n * Assembly graph is in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/assembly_graph.fastg\n * Assembly graph in GFA format is in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa\n======= SPAdes pipeline finished WITH WARNINGS!\n=== Error correction and assembling warnings:\n * 0:00:06.611 33M / 102M WARN General (launcher.cpp : 172) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option.\n======= Warnings saved to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/warnings.log\nSPAdes log can be found here: /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/spades.log\nThank you for using SPAdes!\n\nInsert size mean: 367.3 bp\nInsert size stdev: 37.3 bp\n\n\nCleaning k127 graph\nRepair multi way junctions (2023-10-24 14:41:47)\nFilter by read depth (2023-10-24 14:41:47)\nFilter homopolymer loops (2023-10-24 14:41:47)\nMerge all possible (2023-10-24 14:41:47)\nNormalise read depths (2023-10-24 14:41:47)\nRemove zero length segments (2023-10-24 14:41:47)\nSort link order (2023-10-24 14:41:47)\nGraph cleaning finished (2023-10-24 14:41:47)\nSaving /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2023-10-24 14:41:47)\nFilter by read depth (2023-10-24 14:41:47)\nFilter homopolymer loops (2023-10-24 14:41:47)\nMerge all possible (2023-10-24 14:41:47)\nNormalise read depths (2023-10-24 14:41:47)\nRemove zero length segments (2023-10-24 14:41:47)\nSort link order (2023-10-24 14:41:47)\nGraph cleaning finished (2023-10-24 14:41:47)\nSaving /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/k127_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2023-10-24 14:41:47)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 \n 47 \n 63 \n 77 \n 89 \n 99 \n 107 \n 115 \n 121 \n 127 1 1 5,513 5,513 5,513 0 5.00e-01 <-best\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/\n\n\nDetermining graph multiplicity (2023-10-24 14:41:48)\n Multiplicity is the number of times a sequence occurs in the underlying\nsequence. Single-copy contigs (those with a multiplicity of one, occurring only\nonce in the underlying sequence) are particularly useful.\n Multiplicity determination begins by identifying contigs which are clearly\nsingle-copy because they are of low depth and do not have more than one link\nper side.\n\nMedian depth of 10 longest contigs: 1.00\n\n\nInitial single copy segments:\n 1\n\n Unicycler now uses a greedy algorithm to propagate multiplicity through the\ngraph. For example, if two single-copy contigs merge together, the resulting\ncontig will get a multiplicity of two. When no more propagation is possible,\nadditional single-copy contigs are added and the process is repeated. This\nallows for multiplicity to be correctly assigned to the chromosome (at the\nmedian depth) but also for plasmids (which may be higher or lower in depth).\n\n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n FINDING NEW SINGLE-COPY \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \nREMOVING PROPAGATION TOLERANCE \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n\nSaving /galaxy/server/database/jobs_directory/000/102/working/001_best_spades_graph.gfa\n\n\nCleaning graph (2023-10-24 14:41:48)\n Unicycler now performs various cleaning procedures on the graph to remove\noverlaps and simplify the graph structure. The end result is a graph ready for\nbridging.\n\nGrouping graph edges based on overlap removal\n\r0 / 2 (0.0%)\r1 / 2 (50.0%)\r2 / 2 (100.0%)\n\nRemoving graph overlaps\n\n Bases Bases\n trimmed trimmed\n Segment from from\n number start end\n 1 63 64\nGraph overlaps removed\n\nSaving /galaxy/server/database/jobs_directory/000/102/working/002_overlaps_removed.gfa\n\n Unicycler now selects a set of anchor contigs from the single-copy contigs.\nThese are the contigs which will be connected via bridges to form the final\nassembly.\n\n\n1 anchor segments (5,386 bp) out of 1 total segments (5,386 bp)\n\nAnchor segments:\n 1\n\n\nCreating SPAdes contig bridges (2023-10-24 14:41:48)\n SPAdes uses paired-end information to perform repeat resolution (RR) and\nproduce contigs from the assembly graph. SPAdes saves the graph paths\ncorresponding to these contigs in the contigs.paths file. When one of these\npaths contains two or more anchor contigs, Unicycler can create a bridge from\nthe path.\n\nNo SPAdes contig bridges\n\n\nCreating loop unrolling bridges (2023-10-24 14:41:48)\n When a SPAdes contig path connects an anchor contig with the middle contig\nof a simple loop, Unicycler concludes that the sequences are contiguous (i.e.\nthe loop is not a separate piece of DNA). It then uses the read depth of the\nmiddle and repeat contigs to guess the number of times to traverse the loop and\nmakes a bridge.\n\nNo loop unrolling bridges made\nnone found\n\n\nApplying bridges (2023-10-24 14:41:48)\n Unicycler now applies to the graph in decreasing order of quality. This\nensures that when multiple, contradictory bridges exist, the most supported\noption is used.\n\nBridge type Start -> end Path Quality Result\n\nSaving /galaxy/server/database/jobs_directory/000/102/working/003_bridges_applied.gfa\n\n\nCleaning up leftover segments (2023-10-24 14:41:48)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2023-10-24 14:41:48)\n The assembly is now mostly finished and no more structural changes will be\nmade. Ideally the assembly graph should now have one contig per replicon and no\nerroneous contigs (i.e a complete assembly). If there are more contigs, then\nthe assembly is not complete.\n\nSaving /galaxy/server/database/jobs_directory/000/102/working/004_final_clean.gfa\n\nComponent Segments Links Length N50 Longest segment Status \n 1 1 1 5,386 5,386 5,386 complete\n\n\nRotating completed replicons (2023-10-24 14:41:48)\n Any completed circular contigs (i.e. single contigs which have one link\nconnecting end to start) can have their start position changed without altering\nthe sequence. For consistency, Unicycler now searches for a starting gene (dnaA\nor repA) in each such contig, and if one is found, the contig is rotated to\nstart with that gene on the forward strand.\n\nSegment 1:\n makeblastdb -dbtype nucl -in replicon.fasta\n tblastn -db replicon.fasta -query /usr/local/lib/python3.9/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1\n\nSegment Length Depth Starting gene Position Strand Identity Coverage\n 1 5,386 1.00x none found \n\n\nAssembly complete (2023-10-24 14:41:58)\nSaving /galaxy/server/database/jobs_directory/000/102/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/102/working/assembly.fasta\n\n", "tool_stderr": "tput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\n", "job_stdout": "", "job_stderr": "", "stderr": "tput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\n", "stdout": "\nStarting Unicycler (2023-10-24 14:40:34)\n Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you\nprovided only short reads, Unicycler will essentially function as a SPAdes-\noptimiser. It will try many k-mer sizes, choose the best based on contig length\nand graph connectivity, and scaffold the graph using SPAdes repeat resolution.\n For more information, please see https://github.com/rrwick/Unicycler\n\nCommand: /usr/local/bin/unicycler -t 4 -o ./ --verbosity 3 --pilon_path /usr/local/share/pilon-1.24-0/pilon.jar -1 fq1.fastq -2 fq2.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --no_correct --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --no_pilon --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2\n\nUnicycler version: v0.4.8\nUsing 4 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/102/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 3.14.1 good /usr/local/bin/spades.py \n racon not used \n makeblastdb 2.12.0+ good /usr/local/bin/makeblastdb\n tblastn 2.12.0+ good /usr/local/bin/tblastn \n bowtie2-build not used \n bowtie2 not used \n samtools not used \n java not used \n pilon not used \n bcftools not used \n\n\nChoosing k-mer range for assembly (2023-10-24 14:40:36)\n Unicycler chooses a k-mer range for SPAdes based on the length of the input\nreads. It uses a wide range of many k-mer sizes to maximise the chance of\nfinding an ideal assembly.\n\nSPAdes maximum k-mer: 127\nMedian read length: 251\nK-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127\n\n\nSPAdes assemblies (2023-10-24 14:40:36)\n Unicycler now uses SPAdes to assemble the short reads. It scores the\nassembly graph for each k-mer using the number of contigs (fewer is better) and\nthe number of dead ends (fewer is better). The score function is 1/(c*(d+2)),\nwhere c is the contig count and d is the dead end count.\n\n== Warning == No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly -k 27,47,63,77,89,99,107,115,121,127 --threads 4 --only-assembler -1 /galaxy/server/database/jobs_directory/000/102/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/102/working/fq2.fastq\n\nSystem information:\n SPAdes version: 3.14.1\n Python version: 3.9.9\n OS: Linux-5.10.176+-x86_64-with-glibc2.28\nOutput dir: /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Standard mode\n For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/102/working/fq1.fastq']\n right reads: ['/galaxy/server/database/jobs_directory/000/102/working/fq2.fastq']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27, 47, 63, 77, 89, 99, 107, 115, 121, 127]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/tmp\n Threads: 4\n Memory limit (in Gb): 78\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/spades.log\n/galaxy/server/database/jobs_directory/000/102/working/fq1.fastq: max reads length: 251\n/galaxy/server/database/jobs_directory/000/102/working/fq2.fastq: max reads length: 251\nReads length: 251\n===== Before start started.\n===== Assembling started.\n===== K27 started.\n== Running: /usr/local/bin/spades-core /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K27/configs/config.info\nWARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is tmp_contigs.fasta\n 0:00:00.000 5M / 20M INFO General (main.cpp : 75) Loaded config from /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K27/configs/config.info\n 0:00:00.000 5M / 20M INFO General (memory_limit.cpp : 49) Memory limit set to 78 Gb\n 0:00:00.000 5M / 20M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 5M / 20M INFO General (main.cpp : 86) Maximum k-mer length: 128\n 0:00:00.000 5M / 20M INFO General (main.cpp : 87) Assembling dataset (/galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/dataset.info) with K=27\n 0:00:00.000 5M / 20M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 4\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 194) SPAdes started\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion\n 0:00:00.000 5M / 20M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0\n 0:00:00.000 5M / 20M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.007 5M / 20M INFO General (read_converter.cpp : 73) Converting paired reads\n 0:00:00.107 87M / 87M INFO General (binary_converter.cpp : 111) 7925 reads written\n 0:00:00.108 63M / 63M INFO General (read_converter.cpp : 81) Converting single reads\n 0:00:00.110 73M / 73M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.110 73M / 73M INFO General (read_converter.cpp : 87) Converting merged reads\n 0:00:00.111 73M / 73M INFO General (binary_converter.cpp : 111) 0 reads written\n 0:00:00.152 25M / 29M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction\n 0:00:00.164 25M / 29M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.164 25M / 29M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.164 25M / 29M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting\n 0:00:00.165 25M / 29M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 4 threads. This might take a while.\n 0:00:00.166 25M / 29M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.166 25M / 29M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49995 Gb\n 0:00:00.166 25M / 29M INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304\n 0:00:00.404 42M / 57M INFO General (kmer_splitters.hpp : 293) Used 31700 reads\n 0:00:00.405 42M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:00.487 42M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 35249 kmers in total.\n 0:00:00.488 42M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:00.544 42M / 57M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction\n 0:00:00.545 42M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:00.545 42M / 57M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 4 threads. This might take a while.\n 0:00:00.546 42M / 57M INFO General (file_limit.hpp : 32) Open file limit set to 1048576\n 0:00:00.546 42M / 57M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 6.49992 Gb\n 0:00:00.546 42M / 57M INFO General (kmer_splitters.hpp : 97) Using cell size of 1048576\n 0:00:01.258 3G / 3G INFO General (kmer_splitters.hpp : 364) Processed 35249 kmers\n 0:00:01.258 3G / 3G INFO General (kmer_splitters.hpp : 369) Used 35249 kmers.\n 0:00:01.267 43M / 57M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.\n 0:00:01.615 43M / 57M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 34510 kmers in total.\n 0:00:01.616 43M / 57M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.\n 0:00:01.829 43M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:01.876 39M / 57M INFO General (kmer_index_builder.hpp : 150) Merging final buckets.\n 0:00:01.910 39M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 24880 bytes occupied (5.7676 bits per kmer).\n 0:00:01.910 39M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers\n 0:00:01.916 39M / 57M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.\n 0:00:01.917 39M / 57M INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping\n 0:00:01.918 39M / 57M INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K)\n 0:00:01.918 39M / 57M INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping\n 0:00:01.927 39M / 57M INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 404\n 0:00:01.927 39M / 57M INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 413\n 0:00:01.928 39M / 57M INFO Early tip clipping (early_simplification.hpp : 30) 7414 28-mers were removed by early tip clipper\n 0:00:01.928 39M / 57M INFO General (stage.cpp : 113) PROCEDURE == Condensing graph\n 0:00:01.932 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths\n 0:00:01.937 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2055 sequences extracted\n 0:00:01.940 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops\n 0:00:01.945 39M / 57M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected\n 0:00:01.948 39M / 57M INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)\n 0:00:01.948 39M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index\n 0:00:01.948 39M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices\n 0:00:01.967 40M / 57M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 18528 bytes occupied (4.20506 bits per kmer).\n 0:00:01.967 40M / 57M INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.059 40M / 57M INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM\n 0:00:02.061 40M / 57M INFO General (construction.cpp : 505) Processed 4110 edges\n 0:00:02.068 40M / 57M INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding\n 0:00:02.068 40M / 57M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7\n 0:00:02.069 40M / 57M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 695\n 0:00:02.069 40M / 57M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.069 40M / 57M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model\n 0:00:02.151 40M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2\n 0:00:02.362 40M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4\n 0:00:02.848 40M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8\n 0:00:03.411 40M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16\n 0:00:04.377 40M / 57M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32\n 0:00:04.377 40M / 57M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:04.379 40M / 57M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1\n 0:00:04.379 40M / 57M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 275\n 0:00:04.379 40M / 57M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 275\n 0:00:04.379 40M / 57M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 5132\n 0:00:04.379 40M / 57M INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 671.577\n 0:00:04.379 40M / 57M INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 275\n 0:00:04.380 40M / 57M INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0\n 0:00:04.380 40M / 57M INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification\n 0:00:04.380 40M / 57M INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning\n 0:00:04.380 40M / 57M INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled\n 0:00:04.380 40M / 57M INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover\n 0:00:04.381 40M / 57M INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge r\n..\n overlaps\n 0:00:06.613 33M / 102M INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps\n 0:00:06.613 33M / 102M INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps\n 0:00:06.613 33M / 102M INFO PEResolver (pe_resolver.hpp : 308) Splitting paths\n 0:00:06.613 33M / 102M INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths\n 0:00:06.614 33M / 102M INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 267) Paths finalized\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 439) Closing gaps in paths\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 467) Gap closing completed\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 296) Traversing tandem repeats\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 306) Traversed 0 loops\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 244) Finalizing paths\n 0:00:06.614 33M / 102M INFO General (launcher.cpp : 246) Deduplicating paths\n 0:00:06.615 33M / 102M INFO General (launcher.cpp : 250) Paths deduplicated\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 298) Sorting paths\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps\n 0:00:06.615 33M / 102M INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps\n 0:00:06.615 33M / 102M INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 308) Splitting paths\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths\n 0:00:06.615 33M / 102M INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed\n 0:00:06.615 33M / 102M INFO General (launcher.cpp : 267) Paths finalized\n 0:00:06.616 33M / 102M INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished\n 0:00:06.616 31M / 102M INFO StageManager (stage.cpp : 166) STAGE == Contig Output\n 0:00:06.616 31M / 102M INFO General (contig_output.hpp : 21) Outputting contigs to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/before_rr.fasta\n 0:00:06.624 31M / 102M INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/assembly_graph_with_scaffolds.gfa\n 0:00:06.625 31M / 102M INFO General (contig_output_stage.cpp : 160) Outputting FastG graph to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/assembly_graph.fastg\n 0:00:06.632 31M / 102M INFO General (contig_output_stage.cpp : 190) Breaking scaffolds\n 0:00:06.633 31M / 102M INFO General (contig_output_stage.cpp : 95) Outputting contigs to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/final_contigs.fasta\n 0:00:06.638 31M / 102M INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/final_contigs.paths\n 0:00:06.645 31M / 102M INFO General (contig_output_stage.cpp : 95) Outputting contigs to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/scaffolds.fasta\n 0:00:06.652 31M / 102M INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/scaffolds.paths\n 0:00:06.658 31M / 102M INFO General (contig_output_stage.cpp : 108) Populating GFA with scaffold paths\n 0:00:06.669 31M / 102M INFO General (pipeline.cpp : 259) SPAdes finished\n 0:00:06.674 31M / 102M INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 6 seconds\n===== K127 finished.\n===== Copy files started.\n== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/before_rr.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/before_rr.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/final_contigs.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/contigs.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/strain_graph.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/strain_graph.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/scaffolds.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/scaffolds.fasta /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/scaffolds.paths /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/scaffolds.paths /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/K127/final_contigs.paths /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/contigs.paths\n===== Copy files finished.\n===== Assembling finished.\n===== Breaking scaffolds started.\n== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/scaffolds.fasta --misc_dir /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/misc --threshold_for_breaking_scaffolds 3\n===== Breaking scaffolds finished.\n===== Terminate started.\n===== Terminate finished.\n * Assembled contigs are in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/contigs.fasta\n * Assembled scaffolds are in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/scaffolds.fasta\n * Paths in the assembly graph corresponding to the contigs are in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/contigs.paths\n * Paths in the assembly graph corresponding to the scaffolds are in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/scaffolds.paths\n * Assembly graph is in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/assembly_graph.fastg\n * Assembly graph in GFA format is in /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa\n======= SPAdes pipeline finished WITH WARNINGS!\n=== Error correction and assembling warnings:\n * 0:00:06.611 33M / 102M WARN General (launcher.cpp : 172) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option.\n======= Warnings saved to /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/warnings.log\nSPAdes log can be found here: /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/assembly/spades.log\nThank you for using SPAdes!\n\nInsert size mean: 367.3 bp\nInsert size stdev: 37.3 bp\n\n\nCleaning k127 graph\nRepair multi way junctions (2023-10-24 14:41:47)\nFilter by read depth (2023-10-24 14:41:47)\nFilter homopolymer loops (2023-10-24 14:41:47)\nMerge all possible (2023-10-24 14:41:47)\nNormalise read depths (2023-10-24 14:41:47)\nRemove zero length segments (2023-10-24 14:41:47)\nSort link order (2023-10-24 14:41:47)\nGraph cleaning finished (2023-10-24 14:41:47)\nSaving /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2023-10-24 14:41:47)\nFilter by read depth (2023-10-24 14:41:47)\nFilter homopolymer loops (2023-10-24 14:41:47)\nMerge all possible (2023-10-24 14:41:47)\nNormalise read depths (2023-10-24 14:41:47)\nRemove zero length segments (2023-10-24 14:41:47)\nSort link order (2023-10-24 14:41:47)\nGraph cleaning finished (2023-10-24 14:41:47)\nSaving /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/k127_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2023-10-24 14:41:47)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 \n 47 \n 63 \n 77 \n 89 \n 99 \n 107 \n 115 \n 121 \n 127 1 1 5,513 5,513 5,513 0 5.00e-01 <-best\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/102/working/spades_assembly/\n\n\nDetermining graph multiplicity (2023-10-24 14:41:48)\n Multiplicity is the number of times a sequence occurs in the underlying\nsequence. Single-copy contigs (those with a multiplicity of one, occurring only\nonce in the underlying sequence) are particularly useful.\n Multiplicity determination begins by identifying contigs which are clearly\nsingle-copy because they are of low depth and do not have more than one link\nper side.\n\nMedian depth of 10 longest contigs: 1.00\n\n\nInitial single copy segments:\n 1\n\n Unicycler now uses a greedy algorithm to propagate multiplicity through the\ngraph. For example, if two single-copy contigs merge together, the resulting\ncontig will get a multiplicity of two. When no more propagation is possible,\nadditional single-copy contigs are added and the process is repeated. This\nallows for multiplicity to be correctly assigned to the chromosome (at the\nmedian depth) but also for plasmids (which may be higher or lower in depth).\n\n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n FINDING NEW SINGLE-COPY \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \nREMOVING PROPAGATION TOLERANCE \n MERGING MULTIPLICITY \n SPLITTING MULTIPLICITY \n\nSaving /galaxy/server/database/jobs_directory/000/102/working/001_best_spades_graph.gfa\n\n\nCleaning graph (2023-10-24 14:41:48)\n Unicycler now performs various cleaning procedures on the graph to remove\noverlaps and simplify the graph structure. The end result is a graph ready for\nbridging.\n\nGrouping graph edges based on overlap removal\n\r0 / 2 (0.0%)\r1 / 2 (50.0%)\r2 / 2 (100.0%)\n\nRemoving graph overlaps\n\n Bases Bases\n trimmed trimmed\n Segment from from\n number start end\n 1 63 64\nGraph overlaps removed\n\nSaving /galaxy/server/database/jobs_directory/000/102/working/002_overlaps_removed.gfa\n\n Unicycler now selects a set of anchor contigs from the single-copy contigs.\nThese are the contigs which will be connected via bridges to form the final\nassembly.\n\n\n1 anchor segments (5,386 bp) out of 1 total segments (5,386 bp)\n\nAnchor segments:\n 1\n\n\nCreating SPAdes contig bridges (2023-10-24 14:41:48)\n SPAdes uses paired-end information to perform repeat resolution (RR) and\nproduce contigs from the assembly graph. SPAdes saves the graph paths\ncorresponding to these contigs in the contigs.paths file. When one of these\npaths contains two or more anchor contigs, Unicycler can create a bridge from\nthe path.\n\nNo SPAdes contig bridges\n\n\nCreating loop unrolling bridges (2023-10-24 14:41:48)\n When a SPAdes contig path connects an anchor contig with the middle contig\nof a simple loop, Unicycler concludes that the sequences are contiguous (i.e.\nthe loop is not a separate piece of DNA). It then uses the read depth of the\nmiddle and repeat contigs to guess the number of times to traverse the loop and\nmakes a bridge.\n\nNo loop unrolling bridges made\nnone found\n\n\nApplying bridges (2023-10-24 14:41:48)\n Unicycler now applies to the graph in decreasing order of quality. This\nensures that when multiple, contradictory bridges exist, the most supported\noption is used.\n\nBridge type Start -> end Path Quality Result\n\nSaving /galaxy/server/database/jobs_directory/000/102/working/003_bridges_applied.gfa\n\n\nCleaning up leftover segments (2023-10-24 14:41:48)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2023-10-24 14:41:48)\n The assembly is now mostly finished and no more structural changes will be\nmade. Ideally the assembly graph should now have one contig per replicon and no\nerroneous contigs (i.e a complete assembly). If there are more contigs, then\nthe assembly is not complete.\n\nSaving /galaxy/server/database/jobs_directory/000/102/working/004_final_clean.gfa\n\nComponent Segments Links Length N50 Longest segment Status \n 1 1 1 5,386 5,386 5,386 complete\n\n\nRotating completed replicons (2023-10-24 14:41:48)\n Any completed circular contigs (i.e. single contigs which have one link\nconnecting end to start) can have their start position changed without altering\nthe sequence. For consistency, Unicycler now searches for a starting gene (dnaA\nor repA) in each such contig, and if one is found, the contig is rotated to\nstart with that gene on the forward strand.\n\nSegment 1:\n makeblastdb -dbtype nucl -in replicon.fasta\n tblastn -db replicon.fasta -query /usr/local/lib/python3.9/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1\n\nSegment Length Depth Starting gene Position Strand Identity Coverage\n 1 5,386 1.00x none found \n\n\nAssembly complete (2023-10-24 14:41:58)\nSaving /galaxy/server/database/jobs_directory/000/102/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/102/working/assembly.fasta\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "84.0000000"}, {"title": "Job End Time", "value": "2023-10-24 14:41:58", "plugin": "core", "name": "end_epoch", "raw_value": "1698158518.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:40:34", "plugin": "core", "name": "start_epoch", "raw_value": "1698158434.0000000"}, {"title": "Memory Allocated (MB)", "value": "40000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "40000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "unicycler/0.4.8.0-3", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.4.8.0", "test_index": 3, "time_seconds": 131.46406078338623, "inputs": {"paired_unpaired|fastq_input_selector": "none", "long": {"src": "hda", "id": "453534c33877e79c"}, "min_anchor_seg_len": "10", "spades|kmers": "21,23"}, "job": {"model_class": "Job", "id": "abb793fb51a41ba9", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T14:44:20.083311", "create_time": "2023-10-24T14:42:19.834032", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0", "history_id": "639c57257ba4f009", "external_id": "gxy-c7546", "command_line": "ln -s '/galaxy/server/database/objects/e/5/9/dataset_e59d599d-4133-4830-82a0-1bdae7ade4df.dat' 'lr.fasta' && pilon=`pilon --jar_dir` && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 --pilon_path $pilon -l lr.fasta --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --min_anchor_seg_len '10' --min_kmer_frac '0.2' --max_kmer_frac '0.95' --kmers '21,23' --kmer_count '10' --depth_filter '0.25' --start_gene_id '90.0' --start_gene_cov '95.0' --min_polish_size '1000' --min_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"scores\": \"3,-6,-5,-2\"}", "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", "pilon": "{\"min_polish_size\": \"1000\", \"no_pilon\": \"false\"}", "rotation": "{\"no_rotate\": \"false\", \"start_gene_cov\": \"95.0\", \"start_gene_id\": \"90.0\", \"start_genes\": null}", "spades": "{\"depth_filter\": \"0.25\", \"kmer_count\": \"10\", \"kmers\": \"21,23\", \"largest_component\": \"false\", \"max_kmer_frac\": \"0.95\", \"min_kmer_frac\": \"0.2\", \"no_correct\": \"false\"}", "min_anchor_seg_len": "\"10\"", "linear_seqs": "\"0\"", "min_fasta_length": "\"100\"", "mode": "\"normal\"", "paired_unpaired": "{\"__current_case__\": 3, \"fastq_input_selector\": \"none\"}"}, "inputs": {"long": {"id": "453534c33877e79c", "src": "hda", "uuid": "e59d599d-4133-4830-82a0-1bdae7ade4df"}}, "outputs": {"assembly_graph": {"id": "3b2d2542a772d34e", "src": "hda", "uuid": "80004348-685b-48df-b1af-9ca79a003921"}, "assembly": {"id": "6cbd935e05b789a8", "src": "hda", "uuid": "651e1e76-daad-4623-8dc2-0cfdaa1f81e9"}}, "output_collections": {}, "tool_stdout": "\nStarting Unicycler (2023-10-24 14:44:08)\n Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you\nprovided only long reads, Unicycler will assemble the reads with miniasm and\nthen run repeated polishing rounds using Racon.\n For more information, please see https://github.com/rrwick/Unicycler\n\nCommand: /usr/local/bin/unicycler -t 4 -o ./ --verbosity 3 --pilon_path /usr/local/share/pilon-1.24-0/pilon.jar -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --min_anchor_seg_len 10 --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmers 21,23 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2\n\nUnicycler version: v0.4.8\nUsing 4 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/104/working\n\nDependencies:\n Program Version Status Path \n spades.py not used \n racon 1.4.20 good /usr/local/bin/racon \n makeblastdb 2.12.0+ good /usr/local/bin/makeblastdb\n tblastn 2.12.0+ good /usr/local/bin/tblastn \n bowtie2-build not used \n bowtie2 not used \n samtools not used \n java not used \n pilon not used \n bcftools not used \n\n\nLoading reads (2023-10-24 14:44:09)\n\r0 / 40 (0.0%)\r1 / 40 (2.5%) - 412 bp\r2 / 40 (5.0%) - 4,847 bp\r3 / 40 (7.5%) - 8,974 bp\r4 / 40 (10.0%) - 13,249 bp\r5 / 40 (12.5%) - 14,258 bp\r6 / 40 (15.0%) - 14,806 bp\r7 / 40 (17.5%) - 19,262 bp\r8 / 40 (20.0%) - 19,737 bp\r9 / 40 (22.5%) - 20,395 bp\r10 / 40 (25.0%) - 32,024 bp\r11 / 40 (27.5%) - 32,698 bp\r12 / 40 (30.0%) - 34,509 bp\r13 / 40 (32.5%) - 39,018 bp\r14 / 40 (35.0%) - 43,351 bp\r15 / 40 (37.5%) - 44,224 bp\r16 / 40 (40.0%) - 45,978 bp\r17 / 40 (42.5%) - 46,402 bp\r18 / 40 (45.0%) - 61,596 bp\r19 / 40 (47.5%) - 62,279 bp\r20 / 40 (50.0%) - 63,700 bp\r21 / 40 (52.5%) - 66,412 bp\r22 / 40 (55.0%) - 66,845 bp\r23 / 40 (57.5%) - 67,316 bp\r24 / 40 (60.0%) - 69,428 bp\r25 / 40 (62.5%) - 73,964 bp\r26 / 40 (65.0%) - 75,608 bp\r27 / 40 (67.5%) - 80,223 bp\r28 / 40 (70.0%) - 84,810 bp\r29 / 40 (72.5%) - 92,076 bp\r30 / 40 (75.0%) - 92,832 bp\r31 / 40 (77.5%) - 92,939 bp\r32 / 40 (80.0%) - 93,532 bp\r33 / 40 (82.5%) - 96,370 bp\r34 / 40 (85.0%) - 100,656 bp\r35 / 40 (87.5%) - 119,222 bp\r36 / 40 (90.0%) - 123,827 bp\r37 / 40 (92.5%) - 155,106 bp\r38 / 40 (95.0%) - 156,254 bp\r39 / 40 (97.5%) - 157,993 bp\r40 / 40 (100.0%) - 162,406 bp\r40 / 40 (100.0%) - 162,406 bp\n\n\nAssembling contigs and long reads with miniasm (2023-10-24 14:44:09)\nSaving to /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/01_assembly_reads.fastq:\n 40 long reads\n\nFinding overlaps with minimap... success\n 120 overlaps\n\nAssembling reads with miniasm... success\n 7 segments, 6 links\n\n Unicycler removes any links from the string graph which create branches.\nI.e. if any segment has two or more links connected to one end, those links are\nremoved. This will result in a graph with only simple linear paths that is\nsuitable for creating unambiguous bridges.\n\nNo links needed removal\nSaving /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/11_branching_paths_removed.gfa\nMerging segments into unitigs:\n\nLinear unitig: 3708:125-4288- -> f49b:293-4469+ -> 9e6d:143-4411- -> 9780:142-4271- -> a53e:333-4400+ -> b949:140-4359- -> 054c:932-4389-\n\n 1 linear unitig\n total size = 5,836 bp\nSaving /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/12_unitig_graph.gfa\nSaving /galaxy/server/database/jobs_directory/000/104/working/002_unitig_graph.gfa\n\n\nPolishing miniasm assembly with Racon (2023-10-24 14:44:09)\n Unicycler now uses Racon to polish the miniasm assembly. It does multiple\nrounds of polishing to get the best consensus. Circular unitigs are rotated\nbetween rounds such that all parts (including the ends) are polished well.\n\nSaving to /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/racon_polish/polishing_reads.fastq:\n 40 long reads\n\nPolish Assembly Mapping\nround size 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5.33\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t4010\t+\t1\t6290\t1009\t5054\t2431\t4045\t255\tcm:i:529\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t722\t+\t1\t6290\t5670\t6287\t297\t617\t255\tcm:i:63\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t3632\t4010\t+\t1\t6290\t4\t404\t122\t400\t255\tcm:i:19\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t934\t4391\t-\t1\t6290\t2540\t6287\t2249\t3747\t255\tcm:i:527\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t126\t2508\t-\t1\t6290\t51\t2474\t1276\t2423\t255\tcm:i:245\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t110\t4284\t-\t1\t6290\t4\t4316\t2322\t4312\t255\tcm:i:486\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t2719\t4590\t-\t1\t6290\t4354\t6287\t943\t1933\t255\tcm:i:194\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t116\t4027\t+\t1\t6290\t1774\t6287\t2145\t4513\t255\tcm:i:426\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t2893\t4124\t+\t1\t6290\t4\t1741\t421\t1737\t255\tcm:i:61\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t1345\t4580\t-\t1\t6290\t2854\t6226\t2257\t3372\t255\tcm:i:501\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t98\t2778\t-\t1\t6290\t51\t2831\t1459\t2780\t255\tcm:i:289\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t1225\t4611\t-\t1\t6290\t2825\t6287\t2268\t3462\t255\tcm:i:513\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t97\t2745\t-\t1\t6290\t74\t2805\t1501\t2731\t255\tcm:i:289\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t140\t4284\t-\t1\t6290\t354\t4699\t2022\t4345\t255\tcm:i:377\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t3069\t4304\t-\t1\t6290\t4984\t6271\t614\t1287\t255\tcm:i:117\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t138\t4408\t-\t1\t6290\t72\t4534\t1921\t4462\t255\tcm:i:337\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t3002\t4533\t-\t1\t6290\t4597\t6206\t580\t1609\t255\tcm:i:103\na152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template\t433\t106\t396\t+\t1\t6290\t3083\t3386\t169\t303\t255\tcm:i:32\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t86\t4397\t+\t1\t6290\t1126\t5708\t2368\t4582\t255\tcm:i:487\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t3437\t4392\t+\t1\t6290\t23\t1039\t362\t1016\t255\tcm:i:59\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t86\t539\t+\t1\t6290\t5785\t6254\t217\t469\t255\tcm:i:45\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t105\t4374\t-\t1\t6290\t1806\t6258\t2777\t4452\t255\tcm:i:600\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t105\t1578\t-\t1\t6290\t74\t1603\t761\t1529\t255\tcm:i:150\nbca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template\t1421\t122\t795\t+\t1\t6290\t5209\t5912\t149\t703\t255\tcm:i:24\nbca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template\t1421\t149\t847\t+\t1\t6290\t585\t1307\t155\t722\t255\tcm:i:17\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t93\t4048\t+\t1\t6290\t1886\t6287\t2070\t4401\t255\tcm:i:456\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t2532\t4244\t+\t1\t6290\t4\t1838\t656\t1834\t255\tcm:i:109\nc2f682b3-3774-41a5-8663-32d081b558ee_Basecall_1D_template\t1148\t97\t391\t+\t1\t6290\t2060\t2358\t156\t298\t255\tcm:i:35\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t289\t4485\t+\t1\t6290\t23\t4436\t2106\t4413\t255\tcm:i:421\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t111\t1803\t+\t1\t6290\t4488\t6273\t744\t1785\t255\tcm:i:131\n1 6,290 7.82\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t4010\t+\t1\t6242\t1016\t5009\t2460\t3993\t255\tcm:i:530\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t722\t+\t1\t6242\t5626\t6239\t283\t613\t255\tcm:i:61\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t3632\t4010\t+\t1\t6242\t4\t408\t117\t404\t255\tcm:i:18\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t934\t4391\t-\t1\t6242\t2535\t6239\t2234\t3704\t255\tcm:i:514\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t126\t2508\t-\t1\t6242\t51\t2469\t1387\t2418\t255\tcm:i:271\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t110\t4284\t-\t1\t6242\t4\t4276\t2380\t4272\t255\tcm:i:494\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t2719\t4590\t-\t1\t6242\t4314\t6239\t955\t1925\t255\tcm:i:196\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t108\t4027\t+\t1\t6242\t1759\t6239\t2194\t4480\t255\tcm:i:440\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t2893\t4124\t+\t1\t6242\t4\t1735\t450\t1731\t255\tcm:i:67\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t1345\t4580\t-\t1\t6242\t2848\t6178\t2284\t3330\t255\tcm:i:509\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t98\t2778\t-\t1\t6242\t51\t2825\t1504\t2774\t255\tcm:i:295\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t1225\t4611\t-\t1\t6242\t2819\t6239\t2235\t3420\t255\tcm:i:510\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t109\t2745\t-\t1\t6242\t74\t2787\t1517\t2713\t255\tcm:i:304\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t140\t4284\t-\t1\t6242\t358\t4659\t2051\t4301\t255\tcm:i:391\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t3069\t4304\t-\t1\t6242\t4939\t6223\t618\t1284\t255\tcm:i:114\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t138\t4408\t-\t1\t6242\t72\t4493\t1941\t4421\t255\tcm:i:345\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t3002\t4533\t-\t1\t6242\t4556\t6158\t579\t1602\t255\tcm:i:105\na152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template\t433\t106\t396\t+\t1\t6242\t3077\t3380\t169\t303\t255\tcm:i:32\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t86\t4397\t+\t1\t6242\t1133\t5664\t2405\t4531\t255\tcm:i:507\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t3437\t4397\t+\t1\t6242\t23\t1051\t353\t1028\t255\tcm:i:59\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t107\t539\t+\t1\t6242\t5759\t6206\t204\t447\t255\tcm:i:40\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t105\t4374\t-\t1\t6242\t1799\t6210\t2749\t4411\t255\tcm:i:591\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t105\t1578\t-\t1\t6242\t74\t1601\t795\t1527\t255\tcm:i:165\nbca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template\t1421\t122\t847\t+\t1\t6242\t5166\t5916\t224\t750\t255\tcm:i:35\nbca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template\t1421\t160\t847\t+\t1\t6242\t602\t1310\t144\t708\t255\tcm:i:16\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t124\t4048\t+\t1\t6242\t1908\t6239\t2061\t4331\t255\tcm:i:454\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t2532\t4244\t+\t1\t6242\t4\t1831\t667\t1827\t255\tcm:i:111\nc2f682b3-3774-41a5-8663-32d081b558ee_Basecall_1D_template\t1148\t97\t391\t+\t1\t6242\t2053\t2352\t157\t299\t255\tcm:i:37\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t289\t4485\t+\t1\t6242\t23\t4395\t2130\t4372\t255\tcm:i:425\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t111\t1803\t+\t1\t6242\t4447\t6225\t762\t1778\t255\tcm:i:138\n2 6,242 8.02\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t4010\t+\t1\t6265\t1028\t5025\t2436\t3997\t255\tcm:i:527\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t722\t+\t1\t6265\t5642\t6262\t281\t620\t255\tcm:i:59\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t3632\t4010\t+\t1\t6265\t4\t408\t105\t404\t255\tcm:i:17\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t934\t4391\t-\t1\t6265\t2544\t6262\t2228\t3718\t255\tcm:i:507\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t126\t2508\t-\t1\t6265\t51\t2478\t1353\t2427\t255\tcm:i:260\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t110\t4284\t-\t1\t6265\t4\t4293\t2377\t4289\t255\tcm:i:492\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t2719\t4590\t-\t1\t6265\t4331\t6262\t967\t1931\t255\tcm:i:194\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t108\t4027\t+\t1\t6265\t1772\t6262\t2190\t4490\t255\tcm:i:436\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t2893\t4124\t+\t1\t6265\t4\t1748\t448\t1744\t255\tcm:i:62\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t1345\t4580\t-\t1\t6265\t2857\t6201\t2270\t3344\t255\tcm:i:503\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t98\t2778\t-\t1\t6265\t51\t2834\t1463\t2783\t255\tcm:i:284\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t1225\t4611\t-\t1\t6265\t2828\t6262\t2251\t3434\t255\tcm:i:515\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t102\t2745\t-\t1\t6265\t74\t2804\t1511\t2730\t255\tcm:i:305\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t140\t4284\t-\t1\t6265\t358\t4676\t2063\t4318\t255\tcm:i:392\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t3069\t4328\t-\t1\t6265\t4930\t6246\t623\t1316\t255\tcm:i:113\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t138\t4408\t-\t1\t6265\t72\t4510\t1987\t4438\t255\tcm:i:350\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t3002\t4533\t-\t1\t6265\t4573\t6181\t569\t1608\t255\tcm:i:102\na152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template\t433\t106\t396\t+\t1\t6265\t3089\t3392\t169\t303\t255\tcm:i:32\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t86\t4397\t+\t1\t6265\t1145\t5680\t2423\t4535\t255\tcm:i:509\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t3437\t4397\t+\t1\t6265\t23\t1063\t337\t1040\t255\tcm:i:56\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t107\t539\t+\t1\t6265\t5779\t6229\t223\t450\t255\tcm:i:45\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t105\t4374\t-\t1\t6265\t1812\t6233\t2769\t4421\t255\tcm:i:601\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t105\t1578\t-\t1\t6265\t74\t1615\t764\t1541\t255\tcm:i:156\nbca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template\t1421\t122\t847\t+\t1\t6265\t5182\t5936\t236\t754\t255\tcm:i:36\nbca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template\t1421\t149\t847\t+\t1\t6265\t589\t1322\t155\t733\t255\tcm:i:17\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t124\t4048\t+\t1\t6265\t1921\t6262\t2062\t4341\t255\tcm:i:449\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t2532\t4244\t+\t1\t6265\t4\t1844\t660\t1840\t255\tcm:i:111\nc2f682b3-3774-41a5-8663-32d081b558ee_Basecall_1D_template\t1148\t97\t391\t+\t1\t6265\t2063\t2361\t157\t298\t255\tcm:i:37\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t289\t4485\t+\t1\t6265\t23\t4412\t2182\t4389\t255\tcm:i:436\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t111\t1803\t+\t1\t6265\t4464\t6248\t787\t1784\t255\tcm:i:141\n3 6,265 8.04\n\nBest polish: /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/racon_polish/016_rotated.fasta\nSaving /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/13_racon_polished.gfa\nSaving /galaxy/server/database/jobs_directory/000/104/working/003_racon_polished.gfa\n\n\nAssembly complete (2023-10-24 14:44:10)\nSaving /galaxy/server/database/jobs_directory/000/104/working/assembly.gfa\n\n", "tool_stderr": "tput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\n", "job_stdout": "", "job_stderr": "", "stderr": "tput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\ntput: No value for $TERM and no -T specified\n", "stdout": "\nStarting Unicycler (2023-10-24 14:44:08)\n Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you\nprovided only long reads, Unicycler will assemble the reads with miniasm and\nthen run repeated polishing rounds using Racon.\n For more information, please see https://github.com/rrwick/Unicycler\n\nCommand: /usr/local/bin/unicycler -t 4 -o ./ --verbosity 3 --pilon_path /usr/local/share/pilon-1.24-0/pilon.jar -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --min_anchor_seg_len 10 --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmers 21,23 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2\n\nUnicycler version: v0.4.8\nUsing 4 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/104/working\n\nDependencies:\n Program Version Status Path \n spades.py not used \n racon 1.4.20 good /usr/local/bin/racon \n makeblastdb 2.12.0+ good /usr/local/bin/makeblastdb\n tblastn 2.12.0+ good /usr/local/bin/tblastn \n bowtie2-build not used \n bowtie2 not used \n samtools not used \n java not used \n pilon not used \n bcftools not used \n\n\nLoading reads (2023-10-24 14:44:09)\n\r0 / 40 (0.0%)\r1 / 40 (2.5%) - 412 bp\r2 / 40 (5.0%) - 4,847 bp\r3 / 40 (7.5%) - 8,974 bp\r4 / 40 (10.0%) - 13,249 bp\r5 / 40 (12.5%) - 14,258 bp\r6 / 40 (15.0%) - 14,806 bp\r7 / 40 (17.5%) - 19,262 bp\r8 / 40 (20.0%) - 19,737 bp\r9 / 40 (22.5%) - 20,395 bp\r10 / 40 (25.0%) - 32,024 bp\r11 / 40 (27.5%) - 32,698 bp\r12 / 40 (30.0%) - 34,509 bp\r13 / 40 (32.5%) - 39,018 bp\r14 / 40 (35.0%) - 43,351 bp\r15 / 40 (37.5%) - 44,224 bp\r16 / 40 (40.0%) - 45,978 bp\r17 / 40 (42.5%) - 46,402 bp\r18 / 40 (45.0%) - 61,596 bp\r19 / 40 (47.5%) - 62,279 bp\r20 / 40 (50.0%) - 63,700 bp\r21 / 40 (52.5%) - 66,412 bp\r22 / 40 (55.0%) - 66,845 bp\r23 / 40 (57.5%) - 67,316 bp\r24 / 40 (60.0%) - 69,428 bp\r25 / 40 (62.5%) - 73,964 bp\r26 / 40 (65.0%) - 75,608 bp\r27 / 40 (67.5%) - 80,223 bp\r28 / 40 (70.0%) - 84,810 bp\r29 / 40 (72.5%) - 92,076 bp\r30 / 40 (75.0%) - 92,832 bp\r31 / 40 (77.5%) - 92,939 bp\r32 / 40 (80.0%) - 93,532 bp\r33 / 40 (82.5%) - 96,370 bp\r34 / 40 (85.0%) - 100,656 bp\r35 / 40 (87.5%) - 119,222 bp\r36 / 40 (90.0%) - 123,827 bp\r37 / 40 (92.5%) - 155,106 bp\r38 / 40 (95.0%) - 156,254 bp\r39 / 40 (97.5%) - 157,993 bp\r40 / 40 (100.0%) - 162,406 bp\r40 / 40 (100.0%) - 162,406 bp\n\n\nAssembling contigs and long reads with miniasm (2023-10-24 14:44:09)\nSaving to /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/01_assembly_reads.fastq:\n 40 long reads\n\nFinding overlaps with minimap... success\n 120 overlaps\n\nAssembling reads with miniasm... success\n 7 segments, 6 links\n\n Unicycler removes any links from the string graph which create branches.\nI.e. if any segment has two or more links connected to one end, those links are\nremoved. This will result in a graph with only simple linear paths that is\nsuitable for creating unambiguous bridges.\n\nNo links needed removal\nSaving /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/11_branching_paths_removed.gfa\nMerging segments into unitigs:\n\nLinear unitig: 3708:125-4288- -> f49b:293-4469+ -> 9e6d:143-4411- -> 9780:142-4271- -> a53e:333-4400+ -> b949:140-4359- -> 054c:932-4389-\n\n 1 linear unitig\n total size = 5,836 bp\nSaving /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/12_unitig_graph.gfa\nSaving /galaxy/server/database/jobs_directory/000/104/working/002_unitig_graph.gfa\n\n\nPolishing miniasm assembly with Racon (2023-10-24 14:44:09)\n Unicycler now uses Racon to polish the miniasm assembly. It does multiple\nrounds of polishing to get the best consensus. Circular unitigs are rotated\nbetween rounds such that all parts (including the ends) are polished well.\n\nSaving to /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/racon_polish/polishing_reads.fastq:\n 40 long reads\n\nPolish Assembly Mapping\nround size quality\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t210\t4010\t+\t1\t5836\t1061\t4603\t1147\t3800\t255\tcm:i:200\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t722\t+\t1\t5836\t5221\t5833\t179\t612\t255\tcm:i:27\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t934\t4391\t-\t1\t5836\t2376\t5833\t3457\t3457\t255\tcm:i:1153\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t126\t2525\t-\t1\t5836\t30\t2314\t787\t2399\t255\tcm:i:144\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t280\t4284\t-\t1\t5836\t4\t3936\t1481\t4004\t255\tcm:i:246\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t2719\t4286\t-\t1\t5836\t4215\t5833\t546\t1618\t255\tcm:i:88\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t170\t4027\t+\t1\t5836\t1680\t5833\t1032\t4153\t255\tcm:i:174\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t2893\t4082\t+\t1\t5836\t4\t1602\t220\t1598\t255\tcm:i:30\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t1334\t4566\t-\t1\t5836\t2699\t5786\t1281\t3232\t255\tcm:i:243\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t98\t2778\t-\t1\t5836\t50\t2663\t772\t2680\t255\tcm:i:129\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t1225\t4611\t-\t1\t5836\t2657\t5833\t1469\t3386\t255\tcm:i:268\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t97\t2786\t-\t1\t5836\t30\t2636\t905\t2689\t255\tcm:i:157\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t143\t4271\t-\t1\t5836\t338\t4254\t1834\t4128\t255\tcm:i:470\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t3092\t4330\t-\t1\t5836\t4503\t5798\t430\t1295\t255\tcm:i:77\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t544\t4408\t-\t1\t5836\t69\t3927\t1208\t3864\t255\tcm:i:237\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t3008\t4472\t-\t1\t5836\t4215\t5748\t351\t1533\t255\tcm:i:53\na152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template\t433\t106\t396\t+\t1\t5836\t2909\t3222\t131\t313\t255\tcm:i:22\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t335\t4397\t+\t1\t5836\t1321\t5257\t1351\t4062\t255\tcm:i:280\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t3437\t4349\t+\t1\t5836\t23\t961\t238\t938\t255\tcm:i:40\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t86\t537\t+\t1\t5836\t5334\t5798\t154\t464\t255\tcm:i:26\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t111\t4359\t-\t1\t5836\t1673\t5798\t2062\t4248\t255\tcm:i:487\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t109\t1619\t-\t1\t5836\t30\t1525\t472\t1510\t255\tcm:i:68\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t93\t4048\t+\t1\t5836\t1733\t5833\t1303\t4100\t255\tcm:i:230\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t2532\t4244\t+\t1\t5836\t4\t1690\t311\t1712\t255\tcm:i:43\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t289\t4205\t+\t1\t5836\t23\t3939\t1039\t3916\t255\tcm:i:166\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t296\t1782\t+\t1\t5836\t4242\t5798\t367\t1556\t255\tcm:i:63\nbegin 5,836 5.33\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t4010\t+\t1\t6290\t1009\t5054\t2431\t4045\t255\tcm:i:529\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t722\t+\t1\t6290\t5670\t6287\t297\t617\t255\tcm:i:63\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t3632\t4010\t+\t1\t6290\t4\t404\t122\t400\t255\tcm:i:19\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t934\t4391\t-\t1\t6290\t2540\t6287\t2249\t3747\t255\tcm:i:527\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t126\t2508\t-\t1\t6290\t51\t2474\t1276\t2423\t255\tcm:i:245\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t110\t4284\t-\t1\t6290\t4\t4316\t2322\t4312\t255\tcm:i:486\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t2719\t4590\t-\t1\t6290\t4354\t6287\t943\t1933\t255\tcm:i:194\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t116\t4027\t+\t1\t6290\t1774\t6287\t2145\t4513\t255\tcm:i:426\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t2893\t4124\t+\t1\t6290\t4\t1741\t421\t1737\t255\tcm:i:61\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t1345\t4580\t-\t1\t6290\t2854\t6226\t2257\t3372\t255\tcm:i:501\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t98\t2778\t-\t1\t6290\t51\t2831\t1459\t2780\t255\tcm:i:289\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t1225\t4611\t-\t1\t6290\t2825\t6287\t2268\t3462\t255\tcm:i:513\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t97\t2745\t-\t1\t6290\t74\t2805\t1501\t2731\t255\tcm:i:289\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t140\t4284\t-\t1\t6290\t354\t4699\t2022\t4345\t255\tcm:i:377\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t3069\t4304\t-\t1\t6290\t4984\t6271\t614\t1287\t255\tcm:i:117\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t138\t4408\t-\t1\t6290\t72\t4534\t1921\t4462\t255\tcm:i:337\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t3002\t4533\t-\t1\t6290\t4597\t6206\t580\t1609\t255\tcm:i:103\na152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template\t433\t106\t396\t+\t1\t6290\t3083\t3386\t169\t303\t255\tcm:i:32\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t86\t4397\t+\t1\t6290\t1126\t5708\t2368\t4582\t255\tcm:i:487\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t3437\t4392\t+\t1\t6290\t23\t1039\t362\t1016\t255\tcm:i:59\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t86\t539\t+\t1\t6290\t5785\t6254\t217\t469\t255\tcm:i:45\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t105\t4374\t-\t1\t6290\t1806\t6258\t2777\t4452\t255\tcm:i:600\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t105\t1578\t-\t1\t6290\t74\t1603\t761\t1529\t255\tcm:i:150\nbca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template\t1421\t122\t795\t+\t1\t6290\t5209\t5912\t149\t703\t255\tcm:i:24\nbca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template\t1421\t149\t847\t+\t1\t6290\t585\t1307\t155\t722\t255\tcm:i:17\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t93\t4048\t+\t1\t6290\t1886\t6287\t2070\t4401\t255\tcm:i:456\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t2532\t4244\t+\t1\t6290\t4\t1838\t656\t1834\t255\tcm:i:109\nc2f682b3-3774-41a5-8663-32d081b558ee_Basecall_1D_template\t1148\t97\t391\t+\t1\t6290\t2060\t2358\t156\t298\t255\tcm:i:35\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t289\t4485\t+\t1\t6290\t23\t4436\t2106\t4413\t255\tcm:i:421\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t111\t1803\t+\t1\t6290\t4488\t6273\t744\t1785\t255\tcm:i:131\n1 6,290 7.82\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t4010\t+\t1\t6242\t1016\t5009\t2460\t3993\t255\tcm:i:530\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t129\t722\t+\t1\t6242\t5626\t6239\t283\t613\t255\tcm:i:61\n0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template\t4286\t3632\t4010\t+\t1\t6242\t4\t408\t117\t404\t255\tcm:i:18\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t934\t4391\t-\t1\t6242\t2535\t6239\t2234\t3704\t255\tcm:i:514\n054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template\t4413\t126\t2508\t-\t1\t6242\t51\t2469\t1387\t2418\t255\tcm:i:271\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t110\t4284\t-\t1\t6242\t4\t4276\t2380\t4272\t255\tcm:i:494\n3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template\t4605\t2719\t4590\t-\t1\t6242\t4314\t6239\t955\t1925\t255\tcm:i:196\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t108\t4027\t+\t1\t6242\t1759\t6239\t2194\t4480\t255\tcm:i:440\n4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template\t4127\t2893\t4124\t+\t1\t6242\t4\t1735\t450\t1731\t255\tcm:i:67\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t1345\t4580\t-\t1\t6242\t2848\t6178\t2284\t3330\t255\tcm:i:509\n598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template\t4587\t98\t2778\t-\t1\t6242\t51\t2825\t1504\t2774\t255\tcm:i:295\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t1225\t4611\t-\t1\t6242\t2819\t6239\t2235\t3420\t255\tcm:i:510\n771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template\t4615\t109\t2745\t-\t1\t6242\t74\t2787\t1517\t2713\t255\tcm:i:304\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t140\t4284\t-\t1\t6242\t358\t4659\t2051\t4301\t255\tcm:i:391\n9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template\t4333\t3069\t4304\t-\t1\t6242\t4939\t6223\t618\t1284\t255\tcm:i:114\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t138\t4408\t-\t1\t6242\t72\t4493\t1941\t4421\t255\tcm:i:345\n9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template\t4536\t3002\t4533\t-\t1\t6242\t4556\t6158\t579\t1602\t255\tcm:i:105\na152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template\t433\t106\t396\t+\t1\t6242\t3077\t3380\t169\t303\t255\tcm:i:32\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t86\t4397\t+\t1\t6242\t1133\t5664\t2405\t4531\t255\tcm:i:507\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t3437\t4397\t+\t1\t6242\t23\t1051\t353\t1028\t255\tcm:i:59\na53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template\t4456\t107\t539\t+\t1\t6242\t5759\t6206\t204\t447\t255\tcm:i:40\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t105\t4374\t-\t1\t6242\t1799\t6210\t2749\t4411\t255\tcm:i:591\nb9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template\t4435\t105\t1578\t-\t1\t6242\t74\t1601\t795\t1527\t255\tcm:i:165\nbca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template\t1421\t122\t847\t+\t1\t6242\t5166\t5916\t224\t750\t255\tcm:i:35\nbca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template\t1421\t160\t847\t+\t1\t6242\t602\t1310\t144\t708\t255\tcm:i:16\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t124\t4048\t+\t1\t6242\t1908\t6239\t2061\t4331\t255\tcm:i:454\nbd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template\t4275\t2532\t4244\t+\t1\t6242\t4\t1831\t667\t1827\t255\tcm:i:111\nc2f682b3-3774-41a5-8663-32d081b558ee_Basecall_1D_template\t1148\t97\t391\t+\t1\t6242\t2053\t2352\t157\t299\t255\tcm:i:37\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t289\t4485\t+\t1\t6242\t23\t4395\t2130\t4372\t255\tcm:i:425\nf49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template\t4509\t111\t1803\t+\t1\t6242\t4447\t6225\t762\t1778\t255\tcm:i:138\n2 6,242 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6,265 8.04\n\nBest polish: /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/racon_polish/016_rotated.fasta\nSaving /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/13_racon_polished.gfa\nSaving /galaxy/server/database/jobs_directory/000/104/working/003_racon_polished.gfa\n\n\nAssembly complete (2023-10-24 14:44:10)\nSaving /galaxy/server/database/jobs_directory/000/104/working/assembly.gfa\n\n", "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": "2023-10-24 14:44:10", "plugin": "core", "name": "end_epoch", "raw_value": "1698158650.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 14:44:08", "plugin": "core", "name": "start_epoch", "raw_value": "1698158648.0000000"}, {"title": "Memory Allocated (MB)", "value": "40000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "40000.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "vcfgenotypes/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfgenotypes", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 138.64877104759216, "inputs": {"vcf_input": {"src": "hda", "id": "fb5f2d55884decf8"}}, "job": {"model_class": "Job", "id": "db0a006c0fc0c413", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T13:59:54.217462", "create_time": "2023-10-24T13:57:46.195512", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0", "history_id": "639c57257ba4f009", "external_id": "gxy-89nb5", "command_line": "vcfgenotypes '/galaxy/server/database/objects/c/6/a/dataset_c6a7c714-cb73-4b5b-9fc4-b103ee49b258.dat' > '/galaxy/server/database/objects/e/4/b/dataset_e4bb1cd5-9b51-47a4-9eb0-ce14ee5e632a.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"vcf_input": {"id": "fb5f2d55884decf8", "src": "hda", "uuid": "c6a7c714-cb73-4b5b-9fc4-b103ee49b258"}}, "outputs": {"out_file1": {"id": "0b17ee70b4690eed", "src": "hda", "uuid": "e4bb1cd5-9b51-47a4-9eb0-ce14ee5e632a"}}, "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": "2023-10-24 13:59:43", "plugin": "core", "name": "end_epoch", "raw_value": "1698155983.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 13:59:43", "plugin": "core", "name": "start_epoch", "raw_value": "1698155983.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}], "galaxy_url": "http://34.23.134.173:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.xunit b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.xunit new file mode 100644 index 000000000..d25c7b379 --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/results.xunit @@ -0,0 +1,820 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + >>STAGE: configure[2023-10-24 14:02:08] INFO: Configuring run[2023-10-24 14:02:08] INFO: Total read length: 1466260[2023-10-24 14:02:08] INFO: Input genome size: 10000[2023-10-24 14:02:08] INFO: Estimated coverage: 146[2023-10-24 14:02:08] INFO: Reads N50/N90: 9054 / 4697[2023-10-24 14:02:08] INFO: Minimum overlap set to 5000[2023-10-24 14:02:08] INFO: Selected k-mer size: 15[2023-10-24 14:02:08] INFO: >>>STAGE: assembly[2023-10-24 14:02:08] INFO: Assembling disjointigs[2023-10-24 14:02:08] INFO: Reading sequences[2023-10-24 14:02:08] INFO: Generating solid k-mer index[2023-10-24 14:02:30] INFO: Counting k-mers (1/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:02:30] INFO: Counting k-mers (2/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:02:30] INFO: Filling index table0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:02:55] INFO: Extending reads[2023-10-24 14:02:58] INFO: Overlap-based coverage: 25[2023-10-24 14:02:58] INFO: Median overlap divergence: 0.1692240% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:02:59] INFO: Assembled 1 disjointigs[2023-10-24 14:02:59] INFO: Generating sequence10% 20% 40% 50% 70% 80% 100% [2023-10-24 14:03:00] INFO: >>>STAGE: consensus[2023-10-24 14:03:00] INFO: Running Minimap2[2023-10-24 14:03:01] INFO: Computing consensus[2023-10-24 14:03:02] INFO: Alignment error rate: 0.156879[2023-10-24 14:03:02] INFO: >>>STAGE: repeat[2023-10-24 14:03:02] INFO: Building and resolving repeat graph[2023-10-24 14:03:02] INFO: Reading sequences[2023-10-24 14:03:02] INFO: Building repeat graph50% 100% [2023-10-24 14:03:24] INFO: Median overlap divergence: 0[2023-10-24 14:03:24] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:03:47] INFO: Aligned read sequence: 1184744 / 1313105 (0.902246)[2023-10-24 14:03:47] INFO: Median overlap divergence: 0.0616647[2023-10-24 14:03:47] INFO: Mean edge coverage: 29[2023-10-24 14:03:47] INFO: Resolving repeats[2023-10-24 14:03:47] INFO: >>>STAGE: trestle[2023-10-24 14:03:47] INFO: Simple unbridged repeats: 0[2023-10-24 14:03:47] INFO: Resolved: 0[2023-10-24 14:03:47] INFO: >>>STAGE: contigger[2023-10-24 14:03:47] INFO: Generating contigs[2023-10-24 14:03:47] INFO: Reading sequences[2023-10-24 14:03:47] INFO: Generated 1 contigs[2023-10-24 14:03:47] INFO: Added 0 scaffold connections[2023-10-24 14:03:47] INFO: >>>STAGE: polishing[2023-10-24 14:03:47] INFO: Polishing genome (1/1)[2023-10-24 14:03:47] INFO: Running minimap2Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000a453730000004c'[2023-10-24 14:03:48] INFO: Separating alignment into bubbles[2023-10-24 14:03:49] INFO: Alignment error rate: 0.104507[2023-10-24 14:03:49] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000a4538a0000004d'[2023-10-24 14:03:52] INFO: >>>STAGE: finalize[2023-10-24 14:03:53] INFO: Assembly statistics:Total length:39944Fragments:1Fragments N50:39944Largest frg:39944Scaffolds:0Mean coverage:27[2023-10-24 14:03:53] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/74/working/out_dir/assembly.fasta + ]]> + + + + + + + + >>STAGE: configure[2023-10-24 14:06:07] INFO: Configuring run[2023-10-24 14:06:07] INFO: Total read length: 1466260[2023-10-24 14:06:07] INFO: Input genome size: 10000[2023-10-24 14:06:07] INFO: Estimated coverage: 146[2023-10-24 14:06:07] INFO: Reads N50/N90: 9054 / 4697[2023-10-24 14:06:07] INFO: Minimum overlap set to 5000[2023-10-24 14:06:07] INFO: Selected k-mer size: 15[2023-10-24 14:06:07] INFO: >>>STAGE: assembly[2023-10-24 14:06:07] INFO: Assembling disjointigs[2023-10-24 14:06:07] INFO: Reading sequences[2023-10-24 14:06:07] INFO: Generating solid k-mer index[2023-10-24 14:06:29] INFO: Counting k-mers (1/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:06:29] INFO: Counting k-mers (2/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:06:30] INFO: Filling index table0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:06:54] INFO: Extending reads[2023-10-24 14:06:58] INFO: Overlap-based coverage: 25[2023-10-24 14:06:58] INFO: Median overlap divergence: 0.1692240% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:06:58] INFO: Assembled 1 disjointigs[2023-10-24 14:06:58] INFO: Generating sequence10% 20% 40% 50% 70% 80% 100% [2023-10-24 14:07:00] INFO: >>>STAGE: consensus[2023-10-24 14:07:00] INFO: Running Minimap2[2023-10-24 14:07:00] INFO: Computing consensus[2023-10-24 14:07:01] INFO: Alignment error rate: 0.157030[2023-10-24 14:07:01] INFO: >>>STAGE: repeat[2023-10-24 14:07:01] INFO: Building and resolving repeat graph[2023-10-24 14:07:01] INFO: Reading sequences[2023-10-24 14:07:01] INFO: Building repeat graph50% 100% [2023-10-24 14:07:23] INFO: Median overlap divergence: 0[2023-10-24 14:07:23] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:07:46] INFO: Aligned read sequence: 1184737 / 1313105 (0.902241)[2023-10-24 14:07:46] INFO: Median overlap divergence: 0.0613459[2023-10-24 14:07:46] INFO: Mean edge coverage: 29[2023-10-24 14:07:46] INFO: Resolving repeats[2023-10-24 14:07:46] INFO: >>>STAGE: trestle[2023-10-24 14:07:46] INFO: Simple unbridged repeats: 0[2023-10-24 14:07:46] INFO: Resolved: 0[2023-10-24 14:07:46] INFO: >>>STAGE: contigger[2023-10-24 14:07:46] INFO: Generating contigs[2023-10-24 14:07:46] INFO: Reading sequences[2023-10-24 14:07:46] INFO: Generated 1 contigs[2023-10-24 14:07:46] INFO: Added 0 scaffold connections[2023-10-24 14:07:46] INFO: >>>STAGE: polishing[2023-10-24 14:07:46] INFO: Polishing genome (1/1)[2023-10-24 14:07:46] INFO: Running minimap2Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000a453b500000051'[2023-10-24 14:07:47] INFO: Separating alignment into bubbles[2023-10-24 14:07:48] INFO: Alignment error rate: 0.104939[2023-10-24 14:07:48] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000a453cc00000052'[2023-10-24 14:07:51] INFO: >>>STAGE: finalize[2023-10-24 14:07:51] INFO: Assembly statistics:Total length:40419Fragments:1Fragments N50:40419Largest frg:40419Scaffolds:0Mean coverage:26[2023-10-24 14:07:51] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/76/working/out_dir/assembly.fasta + ]]> + + + + + + + + >>STAGE: configure[2023-10-24 14:10:04] INFO: Configuring run[2023-10-24 14:10:04] INFO: Total read length: 1466260[2023-10-24 14:10:04] INFO: Input genome size: 10000[2023-10-24 14:10:04] INFO: Estimated coverage: 146[2023-10-24 14:10:04] INFO: Reads N50/N90: 9054 / 4697[2023-10-24 14:10:04] INFO: Minimum overlap set to 5000[2023-10-24 14:10:04] INFO: Selected k-mer size: 17[2023-10-24 14:10:04] INFO: Using longest 40x reads for contig assembly[2023-10-24 14:10:04] INFO: >>>STAGE: assembly[2023-10-24 14:10:04] INFO: Assembling disjointigs[2023-10-24 14:10:04] INFO: Reading sequences[2023-10-24 14:10:04] INFO: Generating solid k-mer index[2023-10-24 14:10:26] INFO: Counting k-mers (1/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:10:26] INFO: Counting k-mers (2/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:10:26] INFO: Filling index table0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:10:48] INFO: Extending reads[2023-10-24 14:10:48] INFO: Overlap-based coverage: 3[2023-10-24 14:10:48] INFO: Median overlap divergence: 0.1735210% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:10:48] INFO: Assembled 1 disjointigs[2023-10-24 14:10:48] INFO: Generating sequence10% 20% 40% 50% 70% 80% 100% [2023-10-24 14:10:49] INFO: >>>STAGE: consensus[2023-10-24 14:10:49] INFO: Running Minimap2[2023-10-24 14:10:50] INFO: Computing consensus[2023-10-24 14:10:51] INFO: Alignment error rate: 0.146313[2023-10-24 14:10:51] INFO: >>>STAGE: repeat[2023-10-24 14:10:51] INFO: Building and resolving repeat graph[2023-10-24 14:10:51] INFO: Reading sequences[2023-10-24 14:10:51] INFO: Building repeat graph50% 100% [2023-10-24 14:11:13] INFO: Median overlap divergence: 0[2023-10-24 14:11:13] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:11:36] INFO: Aligned read sequence: 1174263 / 1313105 (0.894264)[2023-10-24 14:11:36] INFO: Median overlap divergence: 0.0589391[2023-10-24 14:11:36] INFO: Mean edge coverage: 29[2023-10-24 14:11:36] INFO: Resolving repeats[2023-10-24 14:11:36] INFO: >>>STAGE: contigger[2023-10-24 14:11:36] INFO: Generating contigs[2023-10-24 14:11:36] INFO: Reading sequences[2023-10-24 14:11:36] INFO: Generated 1 contigs[2023-10-24 14:11:36] INFO: Added 0 scaffold connections[2023-10-24 14:11:36] INFO: >>>STAGE: polishing[2023-10-24 14:11:36] INFO: Polishing genome (1/2)[2023-10-24 14:11:36] INFO: Running minimap2[2023-10-24 14:11:37] INFO: Separating alignment into bubblesTraceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000a453fc00000056'[2023-10-24 14:11:38] INFO: Alignment error rate: 0.099017[2023-10-24 14:11:38] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000a4540e00000057'[2023-10-24 14:11:41] INFO: Polishing genome (2/2)[2023-10-24 14:11:41] INFO: Running minimap2[2023-10-24 14:11:41] INFO: Separating alignment into bubbles[2023-10-24 14:11:42] INFO: Alignment error rate: 0.094400[2023-10-24 14:11:42] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:11:45] INFO: >>>STAGE: finalize[2023-10-24 14:11:45] INFO: Assembly statistics:Total length:40414Fragments:1Fragments N50:40414Largest frg:40414Scaffolds:0Mean coverage:27[2023-10-24 14:11:45] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/78/working/out_dir/assembly.fastaTraceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000a4540f00000059' + ]]> + + + + + + + + >>STAGE: configure[2023-10-24 14:13:56] INFO: Configuring run[2023-10-24 14:13:56] INFO: Total read length: 1466260[2023-10-24 14:13:56] INFO: Input genome size: 10000[2023-10-24 14:13:56] INFO: Estimated coverage: 146[2023-10-24 14:13:56] INFO: Reads N50/N90: 9054 / 4697[2023-10-24 14:13:56] INFO: Minimum overlap set to 5000[2023-10-24 14:13:56] INFO: Selected k-mer size: 15[2023-10-24 14:13:56] INFO: >>>STAGE: assembly[2023-10-24 14:13:56] INFO: Assembling disjointigs[2023-10-24 14:13:56] INFO: Reading sequences[2023-10-24 14:13:56] INFO: Generating solid k-mer index[2023-10-24 14:14:18] INFO: Counting k-mers (1/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:14:18] INFO: Counting k-mers (2/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:14:18] INFO: Filling index table (1/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:14:19] INFO: Filling index table (2/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:14:43] INFO: Extending reads[2023-10-24 14:14:46] INFO: Overlap-based coverage: 24[2023-10-24 14:14:46] INFO: Median overlap divergence: 0.1841870% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:14:47] INFO: Assembled 1 disjointigs[2023-10-24 14:14:47] INFO: Generating sequence10% 20% 30% 40% 50% 60% 70% 80% 100% [2023-10-24 14:14:49] INFO: >>>STAGE: consensus[2023-10-24 14:14:49] INFO: Running Minimap2[2023-10-24 14:14:50] INFO: Computing consensus[2023-10-24 14:14:51] INFO: Alignment error rate: 0.183209[2023-10-24 14:14:51] INFO: >>>STAGE: repeat[2023-10-24 14:14:51] INFO: Building and resolving repeat graph[2023-10-24 14:14:51] INFO: Reading sequences[2023-10-24 14:14:51] INFO: Building repeat graph50% 100% [2023-10-24 14:15:13] INFO: Median overlap divergence: 0[2023-10-24 14:15:13] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2023-10-24 14:15:36] INFO: Aligned read sequence: 1158698 / 1313105 (0.882411)[2023-10-24 14:15:36] INFO: Median overlap divergence: 0.0642069[2023-10-24 14:15:36] INFO: Mean edge coverage: 32[2023-10-24 14:15:36] INFO: Resolving repeats[2023-10-24 14:15:36] INFO: >>>STAGE: plasmids[2023-10-24 14:15:36] INFO: Recovering short unassembled sequencesTraceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000a4543c0000005d'[2023-10-24 14:15:36] INFO: Added 0 extra contigs[2023-10-24 14:15:36] INFO: >>>STAGE: contigger[2023-10-24 14:15:36] INFO: Generating contigs[2023-10-24 14:15:36] INFO: Reading sequences[2023-10-24 14:15:36] INFO: Generated 1 contigs[2023-10-24 14:15:36] INFO: Added 0 scaffold connections[2023-10-24 14:15:36] INFO: >>>STAGE: polishing[2023-10-24 14:15:36] INFO: Polishing genome (1/1)[2023-10-24 14:15:36] INFO: Running minimap2[2023-10-24 14:15:37] INFO: Separating alignment into bubbles[2023-10-24 14:15:38] INFO: Alignment error rate: 0.115105[2023-10-24 14:15:38] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000a4544c0000005e'Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000a454580000005f'[2023-10-24 14:15:42] INFO: >>>STAGE: finalize[2023-10-24 14:15:42] INFO: Assembly statistics:Total length:35685Fragments:1Fragments N50:35685Largest frg:35685Scaffolds:0Mean coverage:36[2023-10-24 14:15:42] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/80/working/out_dir/assembly.fasta + ]]> + + + + + + + + + 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate + ]]> + + + + + + + + 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate + ]]> + + + + + + + + 1 times: 0 (0.00%)Overall alignment rate: 100.00% + ]]> + + + + + + + + 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate + ]]> + + + + + + + + 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate + ]]> + + + + + + + + 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate + ]]> + + + + + + + + 1 times ---- 3 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 3 pairs aligned 0 times concordantly or discordantly; of these: 6 mates make up the pairs; of these: 3 (50.00%) aligned 0 times 3 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times85.00% overall alignment rate + ]]> + + + + + + + + 1 times100.00% overall alignment rate + ]]> + + + + + + + + 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate + ]]> + + + + + + + + + + 1 times ---- 10 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 10 pairs aligned 0 times concordantly or discordantly; of these: 20 mates make up the pairs; of these: 20 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times0.00% overall alignment rate + ]]> + + + + + + + + 1 times ---- 71 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 71 pairs aligned 0 times concordantly or discordantly; of these: 142 mates make up the pairs; of these: 74 (52.11%) aligned 0 times 68 (47.89%) aligned exactly 1 time 0 (0.00%) aligned >1 times92.60% overall alignment rate + ]]> + + + + + + + + 1 times85.80% overall alignment rate + ]]> + + + + + + + + 1 times0.00% overall alignment rate + ]]> + + + + + + + + 1 times ---- 3 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 3 pairs aligned 0 times concordantly or discordantly; of these: 6 mates make up the pairs; of these: 6 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times0.00% overall alignment rate + ]]> + + + + + + + + 1 times85.80% overall alignment rate + ]]> + + + + + + + + 1 times85.80% overall alignment rate + ]]> + + + + + + + + 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + end Path Quality ResultSaving /galaxy/server/database/jobs_directory/000/95/working/003_bridges_applied.gfaCleaning up leftover segments (2023-10-24 14:33:59)Segments eligible for deletion:Bridged assembly graph (2023-10-24 14:33:59) The assembly is now mostly finished and no more structural changes will bemade. Ideally the assembly graph should now have one contig per replicon and noerroneous contigs (i.e a complete assembly). If there are more contigs, thenthe assembly is not complete.Saving /galaxy/server/database/jobs_directory/000/95/working/004_final_clean.gfaComponent Segments Links Length N50 Longest segment Status 1 1 1 5,386 5,386 5,386 completePolishing assembly with Pilon (2023-10-24 14:33:59) Unicycler now conducts multiple rounds of Pilon in an attempt to repair anyremaining small-scale errors with the assembly.Aligning reads to find appropriate insert size range... bowtie2-build 0_insert_size_check.fasta 0_insert_size_check.fasta bowtie2 -1 /galaxy/server/database/jobs_directory/000/95/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/95/working/fq2.fastq -x 0_insert_size_check.fasta --fast --threads 4 -I 0 -X 5000 -S 0_alignments.samInsert size 1st percentile: 263Insert size 99th percentile: 450Pilon polish round 1 bowtie2-build 1_polish_input.fasta 1_polish_input.fasta bowtie2 --local --very-sensitive-local --threads 4 -I 263 -X 450 -x 1_polish_input.fasta -S 1_paired_alignments.sam -1 /galaxy/server/database/jobs_directory/000/95/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/95/working/fq2.fastq samtools sort -@ 4 -o 1_paired_alignments.bam -O bam -T temp 1_paired_alignments.sam samtools index 1_paired_alignments.bam java -jar /usr/local/share/pilon-1.24-0/pilon.jar --genome 1_polish_input.fasta --changes --output 1_pilon --outdir /galaxy/server/database/jobs_directory/000/95/working/pilon_polish --fix bases --frags 1_paired_alignments.bamNo Pilon changesSaving /galaxy/server/database/jobs_directory/000/95/working/005_polished.gfaRotating completed replicons (2023-10-24 14:34:05) Any completed circular contigs (i.e. single contigs which have one linkconnecting end to start) can have their start position changed without alteringthe sequence. For consistency, Unicycler now searches for a starting gene (dnaAor repA) in each such contig, and if one is found, the contig is rotated tostart with that gene on the forward strand.Segment 1: makeblastdb -dbtype nucl -in replicon.fasta tblastn -db replicon.fasta -query /usr/local/lib/python3.9/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1Segment Length Depth Starting gene Position Strand Identity Coverage 1 5,386 1.00x none found Assembly complete (2023-10-24 14:34:20)Saving /galaxy/server/database/jobs_directory/000/95/working/assembly.gfaSaving /galaxy/server/database/jobs_directory/000/95/working/assembly.fasta + ]]> + + + + + + + + C->D and B->C->E) or (A->C->E and B->C->D). Each read which spans such ajunction gets to "vote" for option 1, option 2 or neither. Unicycler creates abridge at each junction for the most voted for option.No suitable two-way junctions present Simple loops are parts of the graph where two contigs (A and B) areconnected via a repeat (C) which loops back to itself (via D). It is possibleto traverse the loop zero times (A->C->B), one time (A->C->D->C->B), two times(A->C->D->C->D->C->B), etc. Long reads which span the loop inform which is thecorrect number of times through. In this step, such reads are found and each isaligned against alternative loop counts. A reads casts its "vote" for the loopcount it agrees best with, and Unicycler creates a bridge using the most votedfor count.No suitable simple loops presentDetermining low score threshold (2023-10-24 14:37:51) Before conducting semi-global alignment of the long reads to the assemblygraph, Unicycler must determine a minimum alignment score threshold such thatnonsense alignments are excluded. To choose a threshold automatically, itexamines alignments between random sequences and selects a score a few standarddeviations above the mean.Automatically choosing a threshold using random alignment scores.Random alignment mean score: 61.66 standard deviation: 1.31 Low score threshold: 61.66 + (7 x 1.31) = 70.86Aligning reads with minimap (2023-10-24 14:37:51)1538655077-153868508050725072255cm:i:9451538650935384-1538650875378291291255cm:i:52Done! 1 out of 1 reads alignedAligning reads (2023-10-24 14:37:51)1/1: 1 (5386 bp)minimap alignments: 5,5077,-,1,8,5080 5093,5384,-,1,5087,5378Reference ranges: 1-: 0 - 5386Range: 1: 0 - 5386 common 10-mers: 5464 line 1: 5076 points, score=5074.000394 (good) line 2: 292 points, score=290.006826 (good)All Seqan alignments (time to align = 0.040 s): Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity 1 0 5085 0 5085 - 15255 100.00 100.00% 1 5085 5386 5085 5386 - 903 100.00 100.00%Final alignments: Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity 1 0 5085 0 5085 - 15255 100.00 100.00% 1 5085 5386 5085 5386 - 903 100.00 100.00%Read alignment summary (2023-10-24 14:37:51)Total read count: 1Fully aligned reads: 1Partially aligned reads: 0Unaligned reads: 0Total bases aligned: 5,386 bpMean alignment identity: 100.0%Deleting /galaxy/server/database/jobs_directory/000/99/working/read_alignment/Setting the minimum scaled score to the 5.0th percentile of full read alignments: 0.00Building long read bridges (2023-10-24 14:37:51) Unicycler uses the long read alignments to produce bridges between anchorsegments. These bridges can be formed using as few as one long read, givingUnicycler the ability to bridge the graph even when long-read depth is low.Median depth of 10 longest contigs: 1.00 Consensus Consensus Target Search Path Best path Best path Best path Best path Start -> end Reads len (bp) time (s) len (bp) Search type time (s) count Best path len (bp) raw score scaled score length disc QualityApplying bridges (2023-10-24 14:37:51) Unicycler now applies to the graph in decreasing order of quality. Thisensures that when multiple, contradictory bridges exist, the most supportedoption is used.Bridge type Start -> end Path Quality ResultSaving /galaxy/server/database/jobs_directory/000/99/working/003_bridges_applied.gfaCleaning up leftover segments (2023-10-24 14:37:51)Segments eligible for deletion:Bridged assembly graph (2023-10-24 14:37:51) The assembly is now mostly finished and no more structural changes will bemade. Ideally the assembly graph should now have one contig per replicon and noerroneous contigs (i.e a complete assembly). If there are more contigs, thenthe assembly is not complete.Saving /galaxy/server/database/jobs_directory/000/99/working/004_final_clean.gfaComponent Segments Links Length N50 Longest segment Status 1 1 1 5,386 5,386 5,386 completePolishing assembly with Pilon (2023-10-24 14:37:51) Unicycler now conducts multiple rounds of Pilon in an attempt to repair anyremaining small-scale errors with the assembly.Aligning reads to find appropriate insert size range... bowtie2-build 0_insert_size_check.fasta 0_insert_size_check.fasta bowtie2 -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz -x 0_insert_size_check.fasta --fast --threads 4 -I 0 -X 5000 -S 0_alignments.samInsert size 1st percentile: 263Insert size 99th percentile: 450Pilon polish round 1 bowtie2-build 1_polish_input.fasta 1_polish_input.fasta bowtie2 --local --very-sensitive-local --threads 4 -I 263 -X 450 -x 1_polish_input.fasta -S 1_paired_alignments.sam -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz samtools sort -@ 4 -o 1_paired_alignments.bam -O bam -T temp 1_paired_alignments.sam samtools index 1_paired_alignments.bam java -jar /usr/local/share/pilon-1.24-0/pilon.jar --genome 1_polish_input.fasta --changes --output 1_pilon --outdir /galaxy/server/database/jobs_directory/000/99/working/pilon_polish --fix bases --frags 1_paired_alignments.bamNo Pilon changesPilon polish round 2 bowtie2-build 2_polish_input.fasta 2_polish_input.fasta bowtie2 --local --very-sensitive-local --threads 4 -I 263 -X 450 -x 2_polish_input.fasta -S 2_paired_alignments.sam -1 /galaxy/server/database/jobs_directory/000/99/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/99/working/fq2.fastq.gz samtools sort -@ 4 -o 2_paired_alignments.bam -O bam -T temp 2_paired_alignments.sam samtools index 2_paired_alignments.bam java -jar /usr/local/share/pilon-1.24-0/pilon.jar --genome 2_polish_input.fasta --changes --output 2_pilon --outdir /galaxy/server/database/jobs_directory/000/99/working/pilon_polish --fix all --frags 2_paired_alignments.bamNo Pilon changesSaving /galaxy/server/database/jobs_directory/000/99/working/005_polished.gfaRotating completed replicons (2023-10-24 14:38:03) Any completed circular contigs (i.e. single contigs which have one linkconnecting end to start) can have their start position changed without alteringthe sequence. For consistency, Unicycler now searches for a starting gene (dnaAor repA) in each such contig, and if one is found, the contig is rotated tostart with that gene on the forward strand.Segment 1: makeblastdb -dbtype nucl -in replicon.fasta tblastn -db replicon.fasta -query /usr/local/lib/python3.9/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1Segment Length Depth Starting gene Position Strand Identity Coverage 1 5,386 1.00x none found Assembly complete (2023-10-24 14:38:13)Saving /galaxy/server/database/jobs_directory/000/99/working/assembly.gfaSaving /galaxy/server/database/jobs_directory/000/99/working/assembly.fasta + ]]> + + + + + + + + end Path Quality ResultSaving /galaxy/server/database/jobs_directory/000/102/working/003_bridges_applied.gfaCleaning up leftover segments (2023-10-24 14:41:48)Segments eligible for deletion:Bridged assembly graph (2023-10-24 14:41:48) The assembly is now mostly finished and no more structural changes will bemade. Ideally the assembly graph should now have one contig per replicon and noerroneous contigs (i.e a complete assembly). If there are more contigs, thenthe assembly is not complete.Saving /galaxy/server/database/jobs_directory/000/102/working/004_final_clean.gfaComponent Segments Links Length N50 Longest segment Status 1 1 1 5,386 5,386 5,386 completeRotating completed replicons (2023-10-24 14:41:48) Any completed circular contigs (i.e. single contigs which have one linkconnecting end to start) can have their start position changed without alteringthe sequence. For consistency, Unicycler now searches for a starting gene (dnaAor repA) in each such contig, and if one is found, the contig is rotated tostart with that gene on the forward strand.Segment 1: makeblastdb -dbtype nucl -in replicon.fasta tblastn -db replicon.fasta -query /usr/local/lib/python3.9/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1Segment Length Depth Starting gene Position Strand Identity Coverage 1 5,386 1.00x none found Assembly complete (2023-10-24 14:41:58)Saving /galaxy/server/database/jobs_directory/000/102/working/assembly.gfaSaving /galaxy/server/database/jobs_directory/000/102/working/assembly.fasta + ]]> + + + + + + + + f49b:293-4469+ -> 9e6d:143-4411- -> 9780:142-4271- -> a53e:333-4400+ -> b949:140-4359- -> 054c:932-4389- 1 linear unitig total size = 5,836 bpSaving /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/12_unitig_graph.gfaSaving /galaxy/server/database/jobs_directory/000/104/working/002_unitig_graph.gfaPolishing miniasm assembly with Racon (2023-10-24 14:44:09) Unicycler now uses Racon to polish the miniasm assembly. It does multiplerounds of polishing to get the best consensus. Circular unitigs are rotatedbetween rounds such that all parts (including the ends) are polished well.Saving to /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/racon_polish/polishing_reads.fastq: 40 long readsPolish Assembly Mappinground size 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6,265 8.04Best polish: /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/racon_polish/016_rotated.fastaSaving /galaxy/server/database/jobs_directory/000/104/working/miniasm_assembly/13_racon_polished.gfaSaving /galaxy/server/database/jobs_directory/000/104/working/003_racon_polished.gfaAssembly complete (2023-10-24 14:44:10)Saving /galaxy/server/database/jobs_directory/000/104/working/assembly.gfa + ]]> + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/tools.yml b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/tools.yml new file mode 100644 index 000000000..e11edc665 --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-24-12-27-1/tools.yml @@ -0,0 +1,92 @@ +chunk: 3 +tools: +- name: split_file_to_collection + owner: bgruening + revisions: + - 6cbe2f30c2d7 + tool_panel_section_label: Collection Operations + tool_shed_url: 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