From 74f170c9119197a8b1b1ca4f7c7edee13872afd3 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 14 Jan 2025 13:43:38 +0000 Subject: [PATCH] Updating anvil-production README for prod-25-01-14-12-34-1 --- reports/anvil-production/README.md | 2 +- .../anvil-production/tool-tests/chunks.json | 10 +- .../prod-25-01-14-12-34-1/chunk.json | 7 + .../prod-25-01-14-12-34-1/chunk.txt | 15 + .../errors/251c84d7eaadebc5.json | 44 + .../errors/2fe056efb5e142a4.json | 44 + .../errors/59c78cc5c60b5503.json | 44 + .../errors/81dc4f6d51ba7b35.json | 44 + .../errors/8b01e92d9d187e3b.json | 44 + .../errors/e693ca82ce43d2f8.json | 82 ++ .../errors/fcce236af6e81fef.json | 44 + .../prod-25-01-14-12-34-1/job-metrics.csv | 208 +++++ .../tool-tests/prod-25-01-14-12-34-1/jobs.txt | 207 +++++ .../prod-25-01-14-12-34-1/results.html | 291 ++++++ .../prod-25-01-14-12-34-1/results.json | 1 + .../prod-25-01-14-12-34-1/results.xunit | 868 ++++++++++++++++++ .../prod-25-01-14-12-34-1/tools.yml | 92 ++ 17 files changed, 2041 insertions(+), 6 deletions(-) create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/chunk.json create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/chunk.txt create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/251c84d7eaadebc5.json create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/2fe056efb5e142a4.json create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/59c78cc5c60b5503.json create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/81dc4f6d51ba7b35.json create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/8b01e92d9d187e3b.json create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/e693ca82ce43d2f8.json create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/fcce236af6e81fef.json create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/job-metrics.csv create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/jobs.txt create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.html create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.json create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.xunit create mode 100644 reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/tools.yml diff --git a/reports/anvil-production/README.md b/reports/anvil-production/README.md index 0d4318360..737e8f7ee 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 Jan 13 00:55:20 2025Mon Jan 06 00:55:00 2025
1ToolsetMon Jan 13 12:53:53 2025Mon Jan 06 12:52:27 2025
2ToolsetTue Jan 14 00:52:23 2025Tue Jan 07 00:52:34 2025
3ToolsetTue Jan 07 12:52:19 2025Tue Dec 31 12:50:39 2024
4ToolsetWed Jan 08 00:51:37 2025Wed Jan 01 00:57:37 2025
5ToolsetWed Jan 08 12:53:47 2025Wed Jan 01 12:50:19 2025
6ToolsetThu Jan 09 00:56:08 2025Thu Jan 02 00:51:03 2025
7ToolsetThu Jan 09 12:52:31 2025Thu Jan 02 12:51:36 2025
8ToolsetFri Jan 10 00:52:36 2025Fri Jan 03 00:51:10 2025
9ToolsetFri Jan 10 12:52:27 2025Fri Jan 03 12:51:00 2025
10ToolsetSat Jan 11 00:52:46 2025Sat Jan 04 00:53:57 2025
11ToolsetSat Jan 11 12:51:24 2025Sat Jan 04 12:49:17 2025
12ToolsetSun Jan 12 00:56:55 2025Sun Jan 05 00:57:37 2025
13ToolsetSun Jan 12 12:49:26 2025Sun Jan 05 12:50:55 2025
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Jan 13 00:55:20 2025Mon Jan 06 00:55:00 2025
1ToolsetMon Jan 13 12:53:53 2025Mon Jan 06 12:52:27 2025
2ToolsetTue Jan 14 00:52:23 2025Tue Jan 07 00:52:34 2025
3ToolsetTue Jan 14 12:50:36 2025Tue Jan 07 12:52:19 2025
4ToolsetWed Jan 08 00:51:37 2025Wed Jan 01 00:57:37 2025
5ToolsetWed Jan 08 12:53:47 2025Wed Jan 01 12:50:19 2025
6ToolsetThu Jan 09 00:56:08 2025Thu Jan 02 00:51:03 2025
7ToolsetThu Jan 09 12:52:31 2025Thu Jan 02 12:51:36 2025
8ToolsetFri Jan 10 00:52:36 2025Fri Jan 03 00:51:10 2025
9ToolsetFri Jan 10 12:52:27 2025Fri Jan 03 12:51:00 2025
10ToolsetSat Jan 11 00:52:46 2025Sat Jan 04 00:53:57 2025
11ToolsetSat Jan 11 12:51:24 2025Sat Jan 04 12:49:17 2025
12ToolsetSun Jan 12 00:56:55 2025Sun Jan 05 00:57:37 2025
13ToolsetSun Jan 12 12:49:26 2025Sun Jan 05 12:50:55 2025
diff --git a/reports/anvil-production/tool-tests/chunks.json b/reports/anvil-production/tool-tests/chunks.json index ae1a0353d..8312163d1 100644 --- a/reports/anvil-production/tool-tests/chunks.json +++ b/reports/anvil-production/tool-tests/chunks.json @@ -28,11 +28,11 @@ "date2": "Sun Jan 05 00:57:37 2025" }, "3": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-07-12-36-1/results.html", - "date1": "Tue Jan 07 12:52:19 2025", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-07-12-36-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/results.html", - "date2": "Tue Dec 31 12:50:39 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.html", + "date1": "Tue Jan 14 12:50:36 2025", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-07-12-36-1/results.html", + "date2": "Tue Jan 07 12:52:19 2025" }, "1": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-13-12-37-1/results.html", diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/chunk.json b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/chunk.json new file mode 100644 index 000000000..12483b75c --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/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/prod-25-01-14-12-34-1/results.html", + "date1": "Tue Jan 14 12:50:36 2025", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/chunk.txt b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/chunk.txt new file mode 100644 index 000000000..780536557 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/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/prod-25-01-14-12-34-1/errors/251c84d7eaadebc5.json b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/251c84d7eaadebc5.json new file mode 100644 index 000000000..f907e89ef --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/251c84d7eaadebc5.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "251c84d7eaadebc5", + "state": "error", + "exit_code": null, + "update_time": "2025-01-14T13:22:44.158163", + "create_time": "2025-01-14T13:22:35.353297", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ddd7b7f231ac291f", + "external_id": "gxy-s4pnc", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/129/registry.xml' '/galaxy/server/database/jobs_directory/000/129/upload_params.json' '155:/galaxy/server/database/objects/8/2/b/dataset_82ba407c-627e-47f2-b937-724058ea8f0e_files:/galaxy/server/database/objects/8/2/b/dataset_82ba407c-627e-47f2-b937-724058ea8f0e.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_ndgduiyv\"", + "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"only_long.fasta\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_1i15hykn\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fasta\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "6bec59745fc6b7fe", + "src": "hda", + "uuid": "82ba407c-627e-47f2-b937-724058ea8f0e" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/2fe056efb5e142a4.json b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/2fe056efb5e142a4.json new file mode 100644 index 000000000..e1441152c --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/2fe056efb5e142a4.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "2fe056efb5e142a4", + "state": "error", + "exit_code": null, + "update_time": "2025-01-14T13:36:23.294083", + "create_time": "2025-01-14T13:36:13.547074", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ddd7b7f231ac291f", + "external_id": "gxy-lhjx4", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/167/registry.xml' '/galaxy/server/database/jobs_directory/000/167/upload_params.json' '211:/galaxy/server/database/objects/5/4/b/dataset_54b83834-efd8-4036-af4f-16b4567d3f70_files:/galaxy/server/database/objects/5/4/b/dataset_54b83834-efd8-4036-af4f-16b4567d3f70.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_16zigu_m\"", + "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"hisat_input_2_forward.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_66s3o4nf\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "afbccd33a8adf6bf", + "src": "hda", + "uuid": "54b83834-efd8-4036-af4f-16b4567d3f70" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/59c78cc5c60b5503.json b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/59c78cc5c60b5503.json new file mode 100644 index 000000000..2b61e2b06 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/59c78cc5c60b5503.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "59c78cc5c60b5503", + "state": "error", + "exit_code": null, + "update_time": "2025-01-14T13:03:29.073933", + "create_time": "2025-01-14T13:03:19.117406", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ddd7b7f231ac291f", + "external_id": "gxy-c6pj4", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/45/registry.xml' '/galaxy/server/database/jobs_directory/000/45/upload_params.json' '52:/galaxy/server/database/objects/a/4/a/dataset_a4a10885-52e8-4312-aef7-b326a3776b75_files:/galaxy/server/database/objects/a/4/a/dataset_a4a10885-52e8-4312-aef7-b326a3776b75.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params__msl4usc\"", + "files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"ecoli_hifi_02.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_zm7j4fxk\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastq.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "b949d99cf2477ca1", + "src": "hda", + "uuid": "a4a10885-52e8-4312-aef7-b326a3776b75" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/81dc4f6d51ba7b35.json b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/81dc4f6d51ba7b35.json new file mode 100644 index 000000000..83e39d458 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/81dc4f6d51ba7b35.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "81dc4f6d51ba7b35", + "state": "error", + "exit_code": null, + "update_time": "2025-01-14T13:08:25.278955", + "create_time": "2025-01-14T13:08:09.756425", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ddd7b7f231ac291f", + "external_id": "gxy-xlvwz", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/86/registry.xml' '/galaxy/server/database/jobs_directory/000/86/upload_params.json' '102:/galaxy/server/database/objects/6/b/7/dataset_6b73af94-8448-419b-b56b-59e492d0ac04_files:/galaxy/server/database/objects/6/b/7/dataset_6b73af94-8448-419b-b56b-59e492d0ac04.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_zgxydc0j\"", + "files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"ecoli_hifi_06.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_wv1_luv7\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastq.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "1bd8cb2f8194097a", + "src": "hda", + "uuid": "6b73af94-8448-419b-b56b-59e492d0ac04" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/8b01e92d9d187e3b.json b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/8b01e92d9d187e3b.json new file mode 100644 index 000000000..2647885e8 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/8b01e92d9d187e3b.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "8b01e92d9d187e3b", + "state": "error", + "exit_code": null, + "update_time": "2025-01-14T12:55:33.007037", + "create_time": "2025-01-14T12:55:24.556132", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ddd7b7f231ac291f", + "external_id": "gxy-8tdjg", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/16/registry.xml' '/galaxy/server/database/jobs_directory/000/16/upload_params.json' '16:/galaxy/server/database/objects/b/c/4/dataset_bc4b82cb-55fe-4cbd-aa11-f33a21f8d455_files:/galaxy/server/database/objects/b/c/4/dataset_bc4b82cb-55fe-4cbd-aa11-f33a21f8d455.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_beck4v4r\"", + "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"test_input_1_a.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_n3rx3hr0\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"bam\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "8b01e92d9d187e3b", + "src": "hda", + "uuid": "bc4b82cb-55fe-4cbd-aa11-f33a21f8d455" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/e693ca82ce43d2f8.json b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/e693ca82ce43d2f8.json new file mode 100644 index 000000000..1f2d29112 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/e693ca82ce43d2f8.json @@ -0,0 +1,82 @@ +{ + "model_class": "Job", + "id": "e693ca82ce43d2f8", + "state": "error", + "exit_code": null, + "update_time": "2025-01-14T13:28:48.505416", + "create_time": "2025-01-14T13:26:15.700977", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0", + "history_id": "ddd7b7f231ac291f", + "external_id": "gxy-hkmrb", + "command_line": "ln -s '/galaxy/server/database/objects/a/8/e/dataset_a8e7667e-3e06-4941-833a-173c42cb310d.dat' fq1.fastq && ln -s '/galaxy/server/database/objects/7/3/8/dataset_738fb138-e581-4661-98b6-3d90bc357e56.dat' fq2.fastq && ln -s '/galaxy/server/database/objects/6/6/4/dataset_664606f8-030b-409a-8205-6ded7a8045fd.dat' 'lr.fasta' && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 -1 'fq1.fastq' -2 'fq2.fastq' -l lr.fasta --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --min_kmer_frac '0.2' --max_kmer_frac '0.95' --kmer_count '10' --depth_filter '0.25' --start_gene_id '90.0' --start_gene_cov '95.0' --min_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2' --keep 2 && mkdir 'spades_graphs' && mv 00*gfa './spades_graphs/' && samtools view -@ \"${GALAXY_SLOTS:-4}\" -u 'read_alignment/long_read_alignments.sam' | samtools sort -@ \"${GALAXY_SLOTS:-4}\" -o 'read_alignment/long_read_alignments.bam'", + "traceback": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "reuse": "[]", + "keep": "\"2\"", + "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"no_simple_bridges\": false, \"scores\": \"3,-6,-5,-2\"}", + "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", + "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\"}", + "min_anchor_seg_len": "\"\"", + "linear_seqs": "\"0\"", + "min_fasta_length": "\"100\"", + "mode": "\"normal\"", + "paired_unpaired": "{\"__current_case__\": 0, \"fastq_input1\": {\"values\": [{\"id\": 175, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 176, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"paired\"}" + }, + "inputs": { + "paired_unpaired|fastq_input1": { + "id": "5b3e62e1ffa8c393", + "src": "hda", + "uuid": "a8e7667e-3e06-4941-833a-173c42cb310d" + }, + "paired_unpaired|fastq_input2": { + "id": "bfcea19bfdadace0", + "src": "hda", + "uuid": "738fb138-e581-4661-98b6-3d90bc357e56" + }, + "long": { + "id": "5aceb46017159497", + "src": "hda", + "uuid": "664606f8-030b-409a-8205-6ded7a8045fd" + } + }, + "outputs": { + "assembly_graph": { + "id": "baaeb697833af929", + "src": "hda", + "uuid": "47cff645-4a58-4097-85ed-8615d0c178f3" + }, + "assembly": { + "id": "ea258d7a926adca1", + "src": "hda", + "uuid": "ab428f4c-4d1c-4507-b764-a1f500f5ccde" + }, + "bam_file": { + "id": "83cc9c9255d88d7e", + "src": "hda", + "uuid": "2f09dae1-4821-4429-84c6-df5b3b7d03ab" + } + }, + "output_collections": { + "spades_collection": { + "id": "7dc5a28cdd92d68e", + "src": "hdca" + } + }, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/fcce236af6e81fef.json b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/fcce236af6e81fef.json new file mode 100644 index 000000000..5b8a4962c --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/errors/fcce236af6e81fef.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "fcce236af6e81fef", + "state": "error", + "exit_code": null, + "update_time": "2025-01-14T13:22:03.034610", + 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2025-01-14T13:03:36.864270 upload1 +59c78cc5c60b5503 error 2025-01-14T13:03:29.073933 upload1 +4916079040ae2744 ok 2025-01-14T13:03:13.822402 toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0 +e5141140bdc944bb ok 2025-01-14T13:01:58.551091 upload1 +7f669389d416e953 ok 2025-01-14T13:01:38.583291 toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0 +93eac48f42b0526e ok 2025-01-14T12:59:55.938577 upload1 +e00cc325c3765d91 ok 2025-01-14T12:59:55.010047 upload1 +5bc4f79361155832 ok 2025-01-14T12:59:54.021468 upload1 +a4bceff17077c16c ok 2025-01-14T12:59:49.082923 upload1 +3472f4585c79a992 ok 2025-01-14T12:59:48.786123 upload1 +254404b1b8312c55 ok 2025-01-14T12:59:46.570847 upload1 +c521f940834b86f0 ok 2025-01-14T12:59:44.493497 upload1 +fd73c40f1dc190e7 ok 2025-01-14T12:59:21.554206 toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0 +ee08340074ef1ddf ok 2025-01-14T12:59:00.184016 upload1 +1048981fa946ba48 ok 2025-01-14T12:58:43.860829 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4 +d7946407b4e9a11b ok 2025-01-14T12:58:31.954225 upload1 +4ef5a5df9765af26 ok 2025-01-14T12:58:14.583583 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4 +a06833697e7d72a0 ok 2025-01-14T12:58:01.873457 upload1 +f271a59afaffc41a ok 2025-01-14T12:58:01.824350 upload1 +d038bc80ccbbc3e3 ok 2025-01-14T12:57:44.080348 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4 +7927fe0f3f95e1d7 ok 2025-01-14T12:57:31.480690 upload1 +20de4c75dc98b309 ok 2025-01-14T12:57:31.474396 upload1 +3fec01478476d6ac ok 2025-01-14T12:57:13.550705 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4 +5f67b4a3e2e5e95e ok 2025-01-14T12:57:01.873931 upload1 +4febfbd22dad2787 ok 2025-01-14T12:57:01.868612 upload1 +bce499b773234192 ok 2025-01-14T12:56:44.048396 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4 +d62bdfde9ea9311b ok 2025-01-14T12:56:18.721131 upload1 +cf188ca2153a5eab ok 2025-01-14T12:56:02.536161 toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5 +a6f61d336c4d2f88 ok 2025-01-14T12:55:48.318985 upload1 +8b01e92d9d187e3b error 2025-01-14T12:55:33.007037 upload1 +fc2ab3a6169d54e0 ok 2025-01-14T12:55:21.928701 toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2 +94b0ed53e44548fc ok 2025-01-14T12:55:09.742000 upload1 +6ce4c19bafedbc85 ok 2025-01-14T12:54:53.436227 toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2 +689a63651735ac2c ok 2025-01-14T12:54:41.453195 upload1 +0478c2ebb76e1267 ok 2025-01-14T12:54:24.944349 toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2 +a2f8c2e12cc20abf ok 2025-01-14T12:54:12.877057 upload1 +1742ddc72b1c4a54 ok 2025-01-14T12:53:56.648163 toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2 +19d7e55009b0dc82 ok 2025-01-14T12:53:39.984272 upload1 +3384ef0dc6714f3c ok 2025-01-14T12:53:39.948901 upload1 +25937eb303c56293 ok 2025-01-14T12:53:19.905428 toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4 +1e6d3865f9715618 ok 2025-01-14T12:53:08.821719 upload1 +7562a391810dacc1 ok 2025-01-14T12:52:54.530866 toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4 +ea8fad58b5ced852 ok 2025-01-14T12:52:43.436549 upload1 +7dc5a28cdd92d68e ok 2025-01-14T12:52:27.179606 toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4 +ddd7b7f231ac291f ok 2025-01-14T12:51:42.850652 upload1 diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.html b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.html new file mode 100644 index 000000000..e45c4e625 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/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/prod-25-01-14-12-34-1/results.json b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.json new file mode 100644 index 000000000..325dd4ccc --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 80, "errors": 26, "failures": 3, "skips": 2}, "tests": [{"id": "bamtools/2.5.2+galaxy2-0", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.5.2+galaxy2", "test_index": 0, "time_seconds": 35.3212194442749, "inputs": {"input_bams": {"src": "hda", "id": "19d7e55009b0dc82"}, "analysis_type|format_type|reference_source|ref_file": {"src": "hda", "id": "3384ef0dc6714f3c"}, "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": "1742ddc72b1c4a54", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:53:56.648163", "create_time": "2025-01-14T12:53:40.467617", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-rq8n2", "command_line": "ln -s '/galaxy/server/database/objects/d/f/1/dataset_df13bb5c-5721-4806-b278-4c78ca42730c.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/b/c/e/metadata_bce86ab4-004f-43cd-804a-5bdbb1237199.dat' localbam.bam.bai && ln -s '/galaxy/server/database/objects/a/f/8/dataset_af8203e0-2ee0-4f6e-b6f1-a4619aab1274.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/b/7/dataset_cb77391f-e368-42d2-80cc-cfcbb10fc6d6.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\": 8, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}}}"}, "inputs": {"analysis_type|format_type|reference_source|ref_file": {"id": "3384ef0dc6714f3c", "src": "hda", "uuid": "af8203e0-2ee0-4f6e-b6f1-a4619aab1274"}, "input_bams": {"id": "19d7e55009b0dc82", "src": "hda", "uuid": "df13bb5c-5721-4806-b278-4c78ca42730c"}}, "outputs": {"out_file1": {"id": "1742ddc72b1c4a54", "src": "hda", "uuid": "cb77391f-e368-42d2-80cc-cfcbb10fc6d6"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Pileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\n", "job_stdout": "", "job_stderr": "", "stderr": "Pileup::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": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-14 12:53:47", "plugin": "core", "name": "end_epoch", "raw_value": "1736859227.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 12:53:47", "plugin": "core", "name": "start_epoch", "raw_value": "1736859227.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bamtools/2.5.2+galaxy2-1", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.5.2+galaxy2", "test_index": 1, "time_seconds": 28.47197699546814, "inputs": {"input_bams": {"src": "hda", "id": "a2f8c2e12cc20abf"}, "analysis_type|analysis_type_selector": "count"}, "job": {"model_class": "Job", "id": "0478c2ebb76e1267", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:54:24.944349", "create_time": "2025-01-14T12:54:13.303098", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-rft9c", "command_line": "ln -s '/galaxy/server/database/objects/7/7/f/dataset_77fe2d7a-881a-4468-b326-c8f5471af699.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/5/c/6/metadata_5c625166-fb1b-44df-86e1-f794cde5529c.dat' localbam.bam.bai && bamtools count > '/galaxy/server/database/objects/1/8/5/dataset_185865e1-27ed-4f91-88fe-763386f6bc45.dat' -in localbam.bam", "traceback": null, "params": {"analysis_type": "{\"__current_case__\": 1, \"analysis_type_selector\": \"count\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"input_bams": {"id": "a2f8c2e12cc20abf", "src": "hda", "uuid": "77fe2d7a-881a-4468-b326-c8f5471af699"}}, "outputs": {"out_file1": {"id": "0478c2ebb76e1267", "src": "hda", "uuid": "185865e1-27ed-4f91-88fe-763386f6bc45"}}, "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": "2025-01-14 12:54:15", "plugin": "core", "name": "end_epoch", "raw_value": "1736859255.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 12:54:15", "plugin": "core", "name": "start_epoch", "raw_value": "1736859255.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bamtools/2.5.2+galaxy2-2", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.5.2+galaxy2", "test_index": 2, "time_seconds": 28.041259288787842, "inputs": {"input_bams": {"src": "hda", "id": "689a63651735ac2c"}, "analysis_type|analysis_type_selector": "coverage"}, "job": {"model_class": "Job", "id": "6ce4c19bafedbc85", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:54:53.436227", "create_time": "2025-01-14T12:54:41.886638", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-twbfb", "command_line": "ln -s '/galaxy/server/database/objects/b/0/b/dataset_b0bb24e9-f6e9-4906-ba11-08a4ce693016.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/8/a/c/metadata_8ac46478-c23d-4e0b-822e-40b579027f25.dat' localbam.bam.bai && bamtools coverage -out '/galaxy/server/database/objects/3/b/8/dataset_3b89b6d2-bb74-4b58-8f12-b5b9c6402397.dat' -in localbam.bam", "traceback": null, "params": {"analysis_type": "{\"__current_case__\": 2, \"analysis_type_selector\": \"coverage\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"input_bams": {"id": "689a63651735ac2c", "src": "hda", "uuid": "b0bb24e9-f6e9-4906-ba11-08a4ce693016"}}, "outputs": {"out_file1": {"id": "6ce4c19bafedbc85", "src": "hda", "uuid": "3b89b6d2-bb74-4b58-8f12-b5b9c6402397"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Pileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\n", "job_stdout": "", "job_stderr": "", "stderr": "Pileup::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": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2025-01-14 12:54:43", "plugin": "core", "name": "end_epoch", "raw_value": "1736859283.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 12:54:43", "plugin": "core", "name": "start_epoch", "raw_value": "1736859283.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bamtools/2.5.2+galaxy2-3", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.5.2+galaxy2", "test_index": 3, "time_seconds": 28.484201431274414, "inputs": {"input_bams": {"src": "hda", "id": "94b0ed53e44548fc"}, "analysis_type|analysis_type_selector": "header"}, "job": {"model_class": "Job", "id": "fc2ab3a6169d54e0", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:55:21.928701", "create_time": "2025-01-14T12:55:10.064035", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-2n4p9", "command_line": "ln -s '/galaxy/server/database/objects/e/7/8/dataset_e7822bc3-f1bf-4e55-9e13-2cdcbf50cad4.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/e/e/2/metadata_ee23f42f-6e1b-44a8-83d0-e30f3bba1fca.dat' localbam.bam.bai && bamtools header > '/galaxy/server/database/objects/3/9/0/dataset_390926fd-09b4-4f86-91c9-83c6754a5f7b.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": "94b0ed53e44548fc", "src": "hda", "uuid": "e7822bc3-f1bf-4e55-9e13-2cdcbf50cad4"}}, "outputs": {"out_file1": {"id": "fc2ab3a6169d54e0", "src": "hda", "uuid": "390926fd-09b4-4f86-91c9-83c6754a5f7b"}}, "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": "2025-01-14 12:55:12", "plugin": "core", "name": "end_epoch", "raw_value": "1736859312.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 12:55:12", "plugin": "core", "name": "start_epoch", "raw_value": "1736859312.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_gtcheck/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_gtcheck", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 40.114062547683716, "inputs": {"input_file": {"src": "hda", "id": "d62bdfde9ea9311b"}}, "job": {"model_class": "Job", "id": "bce499b773234192", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:56:44.048396", "create_time": "2025-01-14T12:56:19.267994", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-phqgj", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/8/7/dataset_f87d2fe3-2fee-41b2-8e5f-2ac6e9ccd69b.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools gtcheck input.vcf.gz > '/galaxy/server/database/objects/f/d/2/dataset_fd2b328e-484f-457d-bbe4-641b85fd6b1e.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_default": "{\"all_sites\": false, \"genotypes\": null, \"homs_only\": false, \"plot\": null, \"query_sample\": null, \"target_sample\": null}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "d62bdfde9ea9311b", "src": "hda", "uuid": "f87d2fe3-2fee-41b2-8e5f-2ac6e9ccd69b"}}, "outputs": {"output_file": {"id": "bce499b773234192", "src": "hda", "uuid": "fd2b328e-484f-457d-bbe4-641b85fd6b1e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO: skipping 11:2343543, monoallelic site. (This is printed only once.)\nINFO:\tTime required to process one record .. 0.000003 seconds\nINFO: skipping 20:271225, not a biallelic site, run `bcftools norm -m -` first. (This is printed only once.)\nINFO: skipping Y:8657215, only diploid FORMAT/PL fields supported. (This is printed only once.)\n", "job_stdout": "", "job_stderr": "", "stderr": "INFO: skipping 11:2343543, monoallelic site. (This is printed only once.)\nINFO:\tTime required to process one record .. 0.000003 seconds\nINFO: skipping 20:271225, not a biallelic site, run `bcftools norm -m -` first. (This is printed only once.)\nINFO: skipping Y:8657215, only diploid FORMAT/PL fields supported. (This is printed only once.)\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": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 12:56:33", "plugin": "core", "name": "start_epoch", "raw_value": "1736859393.0000000"}, {"title": "Job End Time", "value": "2025-01-14 12:56:33", "plugin": "core", "name": "end_epoch", "raw_value": "1736859393.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "bcftools_plugin_tag2tag/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_tag2tag", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 28.18871545791626, "inputs": {"input_file": {"src": "hda", "id": "d7946407b4e9a11b"}, "sec_plugin|conversion": "--gl-to-pl", "sec_plugin|replace": true, "output_type": "v"}, "job": {"model_class": "Job", "id": "1048981fa946ba48", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:58:43.860829", "create_time": "2025-01-14T12:58:32.313592", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-2mq5v", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/9/2/3/dataset_92331ddd-deba-434f-a8a6-eccab33e7262.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/3/5/1/dataset_351ca564-3715-47df-9b30-6bdc17b79dec.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"conversion\": \"--gl-to-pl\", \"replace\": true, \"threshold\": \"0.1\"}", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "d7946407b4e9a11b", "src": "hda", "uuid": "92331ddd-deba-434f-a8a6-eccab33e7262"}}, "outputs": {"output_file": {"id": "1048981fa946ba48", "src": "hda", "uuid": "351ca564-3715-47df-9b30-6bdc17b79dec"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 12:58:34", "plugin": "core", "name": "start_epoch", "raw_value": "1736859514.0000000"}, {"title": "Job End Time", "value": "2025-01-14 12:58:34", "plugin": "core", "name": "end_epoch", "raw_value": "1736859514.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "bcftools_reheader/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_reheader", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 28.471502542495728, "inputs": {"input_file": {"src": "hda", "id": "4febfbd22dad2787"}, "sec_default|header": {"src": "hda", "id": "5f67b4a3e2e5e95e"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "3fec01478476d6ac", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:57:13.550705", "create_time": "2025-01-14T12:57:02.253055", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-4mqw6", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/a/2/4/dataset_a24652b7-2514-4945-bfcc-ea9893490fc0.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools reheader --header \"/galaxy/server/database/objects/c/b/a/dataset_cba94b36-5aec-4891-ab5b-a7efe82e9a0f.dat\" input.vcf.gz | bcftools view --output-type 'v' > '/galaxy/server/database/objects/2/3/a/dataset_23a39467-4300-4a4d-862c-8cc9a542209e.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"header\": {\"values\": [{\"id\": 22, \"src\": \"hda\"}]}, \"rename_samples\": {\"__current_case__\": 0, \"samples_src\": \"none\"}}"}, "inputs": {"input_file": {"id": "4febfbd22dad2787", "src": "hda", "uuid": "a24652b7-2514-4945-bfcc-ea9893490fc0"}, "sec_default|header": {"id": "5f67b4a3e2e5e95e", "src": "hda", "uuid": "cba94b36-5aec-4891-ab5b-a7efe82e9a0f"}}, "outputs": {"output_file": {"id": "3fec01478476d6ac", "src": "hda", "uuid": "23a39467-4300-4a4d-862c-8cc9a542209e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 12:57:03", "plugin": "core", "name": "start_epoch", "raw_value": "1736859423.0000000"}, {"title": "Job End Time", "value": "2025-01-14 12:57:04", "plugin": "core", "name": "end_epoch", "raw_value": "1736859424.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_reheader/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_reheader", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 30.366095304489136, "inputs": {"input_file": {"src": "hda", "id": "20de4c75dc98b309"}, "sec_default|rename_samples|sample_file": {"src": "hda", "id": "7927fe0f3f95e1d7"}, "sec_default|rename_samples|samples_src": "history", "output_type": "v"}, "job": {"model_class": "Job", "id": "d038bc80ccbbc3e3", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:57:44.080348", "create_time": "2025-01-14T12:57:31.924444", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-4jfm2", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/d/f/d/dataset_dfd3560a-555c-4ec9-9cc6-2afb74011d1c.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools reheader --samples \"/galaxy/server/database/objects/c/8/2/dataset_c82510d8-7a14-4477-8932-49c2147833dd.dat\" input.vcf.gz | bcftools view --output-type 'v' > '/galaxy/server/database/objects/2/9/e/dataset_29e4b640-208f-4756-956f-8cbf4d334d79.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "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\": 25, \"src\": \"hda\"}]}, \"samples_src\": \"history\"}}"}, "inputs": {"input_file": {"id": "20de4c75dc98b309", "src": "hda", "uuid": "dfd3560a-555c-4ec9-9cc6-2afb74011d1c"}, "sec_default|rename_samples|sample_file": {"id": "7927fe0f3f95e1d7", "src": "hda", "uuid": "c82510d8-7a14-4477-8932-49c2147833dd"}}, "outputs": {"output_file": {"id": "d038bc80ccbbc3e3", "src": "hda", "uuid": "29e4b640-208f-4756-956f-8cbf4d334d79"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 12:57:34", "plugin": "core", "name": "start_epoch", "raw_value": "1736859454.0000000"}, {"title": "Job End Time", "value": "2025-01-14 12:57:34", "plugin": "core", "name": "end_epoch", "raw_value": "1736859454.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "bcftools_reheader/1.15.1+galaxy4-2", "has_data": true, "data": {"tool_id": "bcftools_reheader", "tool_version": "1.15.1+galaxy4", "test_index": 2, "time_seconds": 30.421849250793457, "inputs": {"input_file": {"src": "hda", "id": "a06833697e7d72a0"}, "sec_default|rename_samples|sample_file": {"src": "hda", "id": "f271a59afaffc41a"}, "sec_default|rename_samples|samples_src": "history", "output_type": "v"}, "job": {"model_class": "Job", "id": "4ef5a5df9765af26", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:58:14.583583", "create_time": "2025-01-14T12:58:02.490339", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-bsrtg", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/c/8/dataset_8c8b9879-b123-49e3-93ba-08e5d1686687.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools reheader --samples \"/galaxy/server/database/objects/a/8/e/dataset_a8ef9b95-98b2-4e1d-9049-a3a580be54f2.dat\" input.vcf.gz | bcftools view --output-type 'v' > '/galaxy/server/database/objects/d/b/c/dataset_dbc7dee0-1625-4165-875c-e4385d7fc10f.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "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\": 28, \"src\": \"hda\"}]}, \"samples_src\": \"history\"}}"}, "inputs": {"input_file": {"id": "a06833697e7d72a0", "src": "hda", "uuid": "8c8b9879-b123-49e3-93ba-08e5d1686687"}, "sec_default|rename_samples|sample_file": {"id": "f271a59afaffc41a", "src": "hda", "uuid": "a8ef9b95-98b2-4e1d-9049-a3a580be54f2"}}, "outputs": {"output_file": {"id": "4ef5a5df9765af26", "src": "hda", "uuid": "dbc7dee0-1625-4165-875c-e4385d7fc10f"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": 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"id": "ea8fad58b5ced852"}, "ref|keep_first": "0", "ref|keep_first_word": false}, "job": {"model_class": "Job", "id": "7562a391810dacc1", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:52:54.530866", "create_time": "2025-01-14T12:52:43.700279", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-728hs", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/5cbde03c1103/fasta_compute_length/fasta_compute_length.py' '/galaxy/server/database/objects/4/1/c/dataset_41cfac83-47b6-4783-b5fa-e45943289f69.dat' '/galaxy/server/database/objects/c/7/5/dataset_c75da079-b18e-4238-af5a-5b304dd11b1b.dat' 0 id_and_desc", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": 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"history_id": "ddd7b7f231ac291f", "external_id": "gxy-9lnvl", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/5cbde03c1103/fasta_compute_length/fasta_compute_length.py' '/galaxy/server/database/objects/b/3/8/dataset_b3846658-3276-4d2a-a419-ac78f6bac35c.dat' '/galaxy/server/database/objects/a/9/f/dataset_a9f6b69d-c783-4437-98b0-47c83a513fc9.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\": 5, \"src\": \"hda\"}]}, \"keep_first\": \"14\", \"keep_first_word\": false, \"ref_source\": \"history\"}"}, "inputs": {"ref|input": {"id": "1e6d3865f9715618", "src": "hda", "uuid": "b3846658-3276-4d2a-a419-ac78f6bac35c"}}, "outputs": {"output": {"id": "25937eb303c56293", "src": "hda", "uuid": "a9f6b69d-c783-4437-98b0-47c83a513fc9"}}, "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": "2025-01-14 12:53:10", "plugin": "core", "name": "end_epoch", "raw_value": "1736859190.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 12:53:10", "plugin": "core", "name": "start_epoch", "raw_value": "1736859190.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fasta_compute_length/1.0.4-3", "has_data": true, "data": {"tool_id": "fasta_compute_length", "tool_version": "1.0.4", "test_index": 3, "status": "skip"}}, {"id": "fasta_compute_length/1.0.4-4", "has_data": true, "data": {"tool_id": "fasta_compute_length", "tool_version": "1.0.4", "test_index": 4, "status": "skip"}}, {"id": "flye/2.9.5+galaxy0-0", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.9.5+galaxy0", "test_index": 0, "time_seconds": 139.4083981513977, "inputs": {"inputs": [{"src": "hda", "id": "c521f940834b86f0"}, {"src": "hda", "id": "254404b1b8312c55"}, {"src": "hda", "id": "3472f4585c79a992"}, {"src": "hda", "id": "a4bceff17077c16c"}, {"src": "hda", "id": "5bc4f79361155832"}, {"src": "hda", "id": "e00cc325c3765d91"}, {"src": "hda", "id": "93eac48f42b0526e"}], "mode_conditional|mode": "--pacbio-raw", "iterations": "0", "generate_log": true}, "job": {"model_class": "Job", "id": "7f669389d416e953", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:01:38.583291", "create_time": "2025-01-14T12:59:56.396358", "galaxy_version": "23.1", "command_version": "2.9.5-b1801", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-7cghq", "command_line": "ln -sf '/galaxy/server/database/objects/b/3/0/dataset_b3002c54-8767-4e1f-b771-276707433393.dat' ./input_0.fastq.gz && ln -sf '/galaxy/server/database/objects/5/4/8/dataset_548fc57e-6fd9-48e0-a341-de8277055060.dat' ./input_1.fastq.gz && ln -sf '/galaxy/server/database/objects/1/4/1/dataset_14102ec9-26e5-4518-a281-ba4cbe51b4a1.dat' ./input_2.fastq.gz && ln -sf '/galaxy/server/database/objects/b/c/0/dataset_bc099286-b7ce-4ff9-b6f6-1790ba6b1470.dat' ./input_3.fastq.gz && ln -sf '/galaxy/server/database/objects/c/b/2/dataset_cb208669-d39b-4f04-acaf-fad4da7487f1.dat' ./input_4.fastq.gz && ln -sf '/galaxy/server/database/objects/c/5/2/dataset_c5273fd0-fa58-4431-8dcf-030f5b0fbcb6.dat' ./input_5.fastq.gz && ln -sf '/galaxy/server/database/objects/b/8/e/dataset_b8e41c95-c923-4c28-b15b-989ae321cdd8.dat' ./input_6.fastq.gz && flye --pacbio-raw ./input_0.fastq.gz ./input_1.fastq.gz ./input_2.fastq.gz ./input_3.fastq.gz ./input_4.fastq.gz ./input_5.fastq.gz ./input_6.fastq.gz -o out_dir -t ${GALAXY_SLOTS:-4} -i 0", "traceback": null, "params": {"mode_conditional": "{\"__current_case__\": 3, \"mode\": \"--pacbio-raw\"}", "iterations": "\"0\"", "min_overlap": "\"\"", "keep_haplotypes": "false", "scaffold": "false", "meta": "false", "asm": "{\"__current_case__\": 1, \"asm_select\": \"false\"}", "no_alt_contigs": "false", "generate_log": "true", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"inputs": {"id": "c521f940834b86f0", "src": "hda", "uuid": "b3002c54-8767-4e1f-b771-276707433393"}, "inputs1": {"id": "c521f940834b86f0", "src": "hda", "uuid": "b3002c54-8767-4e1f-b771-276707433393"}, "inputs2": {"id": "254404b1b8312c55", "src": "hda", "uuid": "548fc57e-6fd9-48e0-a341-de8277055060"}, "inputs3": {"id": "3472f4585c79a992", "src": "hda", "uuid": "14102ec9-26e5-4518-a281-ba4cbe51b4a1"}, "inputs4": {"id": "a4bceff17077c16c", "src": "hda", "uuid": "bc099286-b7ce-4ff9-b6f6-1790ba6b1470"}, "inputs5": {"id": "5bc4f79361155832", "src": "hda", "uuid": "cb208669-d39b-4f04-acaf-fad4da7487f1"}, "inputs6": {"id": "e00cc325c3765d91", "src": "hda", "uuid": "c5273fd0-fa58-4431-8dcf-030f5b0fbcb6"}, "inputs7": {"id": "93eac48f42b0526e", "src": "hda", "uuid": "b8e41c95-c923-4c28-b15b-989ae321cdd8"}}, "outputs": {"consensus": {"id": "7f669389d416e953", "src": "hda", "uuid": "a2b8c240-fda9-405b-8beb-25025c6e779d"}, "assembly_graph": {"id": "e5141140bdc944bb", "src": "hda", "uuid": "4c31717f-fb05-48dd-a4a1-999ac97959d7"}, "assembly_gfa": {"id": "4916079040ae2744", "src": "hda", "uuid": "4377ce4f-4c59-48f1-b490-472efb025d23"}, "assembly_info": {"id": "09c2bea67e1bd83d", "src": "hda", "uuid": "368010a8-760b-40c5-bbf6-2d62a3d879fd"}, "flye_log": {"id": "59c78cc5c60b5503", "src": "hda", "uuid": "bfe80f88-d0b5-4bfb-9c8a-ae495f39416f"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[2025-01-14 13:00:18] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:00:18] INFO: >>>STAGE: configure\n[2025-01-14 13:00:18] INFO: Configuring run\n[2025-01-14 13:00:18] INFO: Total read length: 7249289\n[2025-01-14 13:00:18] INFO: Reads N50/N90: 11150 / 5790\n[2025-01-14 13:00:18] INFO: Minimum overlap set to 6000\n[2025-01-14 13:00:18] INFO: >>>STAGE: assembly\n[2025-01-14 13:00:18] INFO: Assembling disjointigs\n[2025-01-14 13:00:18] INFO: Reading sequences\n[2025-01-14 13:00:23] INFO: Counting k-mers:\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:01:14] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:01:14] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:01:16] INFO: Extending reads\n[2025-01-14 13:01:19] INFO: Overlap-based coverage: 10\n[2025-01-14 13:01:19] INFO: Median overlap divergence: 0.235584\n0% 80% 90% 100% \n[2025-01-14 13:01:19] INFO: Assembled 2 disjointigs\n[2025-01-14 13:01:19] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:01:20] INFO: Filtering contained disjointigs\n0% 50% 100% \n[2025-01-14 13:01:20] INFO: Contained seqs: 0\n[2025-01-14 13:01:20] INFO: >>>STAGE: consensus\n[2025-01-14 13:01:20] INFO: Running Minimap2\n[2025-01-14 13:01:21] INFO: Computing consensus\n[2025-01-14 13:01:26] INFO: Alignment error rate: 0.196790\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/41/tmp/pymp-d5yqrrz6'\n[2025-01-14 13:01:26] INFO: >>>STAGE: repeat\n[2025-01-14 13:01:26] INFO: Building and resolving repeat graph\n[2025-01-14 13:01:26] INFO: Parsing disjointigs\n[2025-01-14 13:01:26] INFO: Building repeat graph\n0% 50% 100% \n[2025-01-14 13:01:27] INFO: Median overlap divergence: 0.0761919\n[2025-01-14 13:01:27] INFO: Parsing reads\n[2025-01-14 13:01:27] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:01:28] INFO: Aligned read sequence: 6325338 / 6471580 (0.977402)\n[2025-01-14 13:01:28] INFO: Median overlap divergence: 0.130431\n[2025-01-14 13:01:28] INFO: Mean edge coverage: 14\n[2025-01-14 13:01:28] INFO: Simplifying the graph\n[2025-01-14 13:01:28] INFO: >>>STAGE: contigger\n[2025-01-14 13:01:28] INFO: Generating contigs\n[2025-01-14 13:01:28] INFO: Reading sequences\n[2025-01-14 13:01:28] INFO: Generated 1 contigs\n[2025-01-14 13:01:28] INFO: Added 0 scaffold connections\n[2025-01-14 13:01:28] INFO: >>>STAGE: finalize\n[2025-01-14 13:01:28] INFO: Assembly statistics:\n\n\tTotal length:\t419793\n\tFragments:\t1\n\tFragments N50:\t419793\n\tLargest frg:\t419793\n\tScaffolds:\t0\n\tMean coverage:\t14\n\n[2025-01-14 13:01:28] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/41/working/out_dir/assembly.fasta\n", "job_stdout": "", "job_stderr": "", "stderr": "[2025-01-14 13:00:18] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:00:18] INFO: >>>STAGE: configure\n[2025-01-14 13:00:18] INFO: Configuring run\n[2025-01-14 13:00:18] INFO: Total read length: 7249289\n[2025-01-14 13:00:18] INFO: Reads N50/N90: 11150 / 5790\n[2025-01-14 13:00:18] INFO: Minimum overlap set to 6000\n[2025-01-14 13:00:18] INFO: >>>STAGE: assembly\n[2025-01-14 13:00:18] INFO: Assembling disjointigs\n[2025-01-14 13:00:18] INFO: Reading sequences\n[2025-01-14 13:00:23] INFO: Counting k-mers:\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:01:14] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:01:14] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:01:16] INFO: Extending reads\n[2025-01-14 13:01:19] INFO: Overlap-based coverage: 10\n[2025-01-14 13:01:19] INFO: Median overlap divergence: 0.235584\n0% 80% 90% 100% \n[2025-01-14 13:01:19] INFO: Assembled 2 disjointigs\n[2025-01-14 13:01:19] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:01:20] INFO: Filtering contained disjointigs\n0% 50% 100% \n[2025-01-14 13:01:20] INFO: Contained seqs: 0\n[2025-01-14 13:01:20] INFO: >>>STAGE: consensus\n[2025-01-14 13:01:20] INFO: Running Minimap2\n[2025-01-14 13:01:21] INFO: Computing consensus\n[2025-01-14 13:01:26] INFO: Alignment error rate: 0.196790\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/41/tmp/pymp-d5yqrrz6'\n[2025-01-14 13:01:26] INFO: >>>STAGE: repeat\n[2025-01-14 13:01:26] INFO: Building and resolving repeat graph\n[2025-01-14 13:01:26] INFO: Parsing disjointigs\n[2025-01-14 13:01:26] INFO: Building repeat graph\n0% 50% 100% \n[2025-01-14 13:01:27] INFO: Median overlap divergence: 0.0761919\n[2025-01-14 13:01:27] INFO: Parsing reads\n[2025-01-14 13:01:27] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:01:28] INFO: Aligned read sequence: 6325338 / 6471580 (0.977402)\n[2025-01-14 13:01:28] INFO: Median overlap divergence: 0.130431\n[2025-01-14 13:01:28] INFO: Mean edge coverage: 14\n[2025-01-14 13:01:28] INFO: Simplifying the graph\n[2025-01-14 13:01:28] INFO: >>>STAGE: contigger\n[2025-01-14 13:01:28] INFO: Generating contigs\n[2025-01-14 13:01:28] INFO: Reading sequences\n[2025-01-14 13:01:28] INFO: Generated 1 contigs\n[2025-01-14 13:01:28] INFO: Added 0 scaffold connections\n[2025-01-14 13:01:28] INFO: >>>STAGE: finalize\n[2025-01-14 13:01:28] INFO: Assembly statistics:\n\n\tTotal length:\t419793\n\tFragments:\t1\n\tFragments N50:\t419793\n\tLargest frg:\t419793\n\tScaffolds:\t0\n\tMean coverage:\t14\n\n[2025-01-14 13:01:28] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/41/working/out_dir/assembly.fasta\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:00:18", "plugin": "core", "name": "start_epoch", "raw_value": "1736859618.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:01:28", "plugin": "core", "name": "end_epoch", "raw_value": "1736859688.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "70.0000000"}]}, "status": "success"}}, {"id": "flye/2.9.5+galaxy0-1", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.9.5+galaxy0", "test_index": 1, "time_seconds": 93.77630543708801, "inputs": {"inputs": {"src": "hda", "id": "845295c9499631b3"}, "mode_conditional|mode": "--nano-raw", "iterations": "0"}, "job": {"model_class": "Job", "id": "4916079040ae2744", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:03:13.822402", "create_time": "2025-01-14T13:01:58.889293", "galaxy_version": "23.1", "command_version": "2.9.5-b1801", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-rl4rr", "command_line": "ln -sf '/galaxy/server/database/objects/c/f/6/dataset_cf604b3f-b6a2-4cdf-b57e-99532979650e.dat' ./input_0.fasta.gz && flye --nano-raw ./input_0.fasta.gz -o out_dir -t ${GALAXY_SLOTS:-4} -i 0", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "generate_log": "false", "no_alt_contigs": "false", "asm": "{\"__current_case__\": 1, \"asm_select\": \"false\"}", "meta": "false", "scaffold": "false", "keep_haplotypes": "false", "min_overlap": "\"\"", "iterations": "\"0\"", "mode_conditional": "{\"__current_case__\": 0, \"mode\": \"--nano-raw\"}"}, "inputs": {"inputs1": {"id": "845295c9499631b3", "src": "hda", "uuid": "cf604b3f-b6a2-4cdf-b57e-99532979650e"}, "inputs": {"id": "845295c9499631b3", "src": "hda", "uuid": "cf604b3f-b6a2-4cdf-b57e-99532979650e"}}, "outputs": {"consensus": {"id": "83392d55fd58fb6b", "src": "hda", "uuid": "1bf24181-245c-4598-ace1-454c6a46a74d"}, "assembly_graph": {"id": "5cd47cdeb53b379d", "src": "hda", "uuid": "b28a93d0-4309-4136-8375-7a732e3fb140"}, "assembly_gfa": {"id": "c682cfb22dbc52b4", "src": "hda", "uuid": "1a4630e0-db01-4533-bcce-0a5367b2d8f8"}, "assembly_info": {"id": "a029e097ca192eef", "src": "hda", "uuid": "34910281-3a6e-47f4-846c-f9fd60baea5c"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[2025-01-14 13:02:01] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:02:01] INFO: >>>STAGE: configure\n[2025-01-14 13:02:01] INFO: Configuring run\n[2025-01-14 13:02:01] INFO: Total read length: 1466260\n[2025-01-14 13:02:01] INFO: Reads N50/N90: 9054 / 4697\n[2025-01-14 13:02:01] INFO: Minimum overlap set to 5000\n[2025-01-14 13:02:01] INFO: >>>STAGE: assembly\n[2025-01-14 13:02:01] INFO: Assembling disjointigs\n[2025-01-14 13:02:01] INFO: Reading sequences\n[2025-01-14 13:02:05] INFO: Counting k-mers:\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:02:56] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:02:56] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:03:00] INFO: Extending reads\n[2025-01-14 13:03:03] INFO: Overlap-based coverage: 42\n[2025-01-14 13:03:03] INFO: Median overlap divergence: 0.105617\n0% 90% 100% \n[2025-01-14 13:03:03] INFO: Assembled 1 disjointigs\n[2025-01-14 13:03:03] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:03:03] INFO: Filtering contained disjointigs\n0% 100% \n[2025-01-14 13:03:03] INFO: Contained seqs: 0\n[2025-01-14 13:03:04] INFO: >>>STAGE: consensus\n[2025-01-14 13:03:04] INFO: Running Minimap2\n[2025-01-14 13:03:04] INFO: Computing consensus\n[2025-01-14 13:03:05] INFO: Alignment error rate: 0.175120\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/43/tmp/pymp-c5kjtoiw'\n[2025-01-14 13:03:05] INFO: >>>STAGE: repeat\n[2025-01-14 13:03:05] INFO: Building and resolving repeat graph\n[2025-01-14 13:03:05] INFO: Parsing disjointigs\n[2025-01-14 13:03:05] INFO: Building repeat graph\n0% 100% \n[2025-01-14 13:03:05] INFO: Median overlap divergence: 0.0151003\n[2025-01-14 13:03:05] INFO: Parsing reads\n[2025-01-14 13:03:05] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:03:05] INFO: Aligned read sequence: 1166207 / 1313105 (0.888129)\n[2025-01-14 13:03:05] INFO: Median overlap divergence: 0.0550349\n[2025-01-14 13:03:05] INFO: Mean edge coverage: 33\n[2025-01-14 13:03:05] INFO: Simplifying the graph\n[2025-01-14 13:03:05] INFO: >>>STAGE: contigger\n[2025-01-14 13:03:05] INFO: Generating contigs\n[2025-01-14 13:03:05] INFO: Reading sequences\n[2025-01-14 13:03:05] INFO: Generated 3 contigs\n[2025-01-14 13:03:05] INFO: Added 0 scaffold connections\n[2025-01-14 13:03:05] INFO: >>>STAGE: finalize\n[2025-01-14 13:03:05] INFO: Assembly statistics:\n\n\tTotal length:\t34929\n\tFragments:\t3\n\tFragments N50:\t21816\n\tLargest frg:\t21816\n\tScaffolds:\t0\n\tMean coverage:\t34\n\n[2025-01-14 13:03:05] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/43/working/out_dir/assembly.fasta\n", "job_stdout": "", "job_stderr": "", "stderr": "[2025-01-14 13:02:01] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:02:01] INFO: >>>STAGE: configure\n[2025-01-14 13:02:01] INFO: Configuring run\n[2025-01-14 13:02:01] INFO: Total read length: 1466260\n[2025-01-14 13:02:01] INFO: Reads N50/N90: 9054 / 4697\n[2025-01-14 13:02:01] INFO: Minimum overlap set to 5000\n[2025-01-14 13:02:01] INFO: >>>STAGE: assembly\n[2025-01-14 13:02:01] INFO: Assembling disjointigs\n[2025-01-14 13:02:01] INFO: Reading sequences\n[2025-01-14 13:02:05] INFO: Counting k-mers:\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:02:56] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:02:56] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:03:00] INFO: Extending reads\n[2025-01-14 13:03:03] INFO: Overlap-based coverage: 42\n[2025-01-14 13:03:03] INFO: Median overlap divergence: 0.105617\n0% 90% 100% \n[2025-01-14 13:03:03] INFO: Assembled 1 disjointigs\n[2025-01-14 13:03:03] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:03:03] INFO: Filtering contained disjointigs\n0% 100% \n[2025-01-14 13:03:03] INFO: Contained seqs: 0\n[2025-01-14 13:03:04] INFO: >>>STAGE: consensus\n[2025-01-14 13:03:04] INFO: Running Minimap2\n[2025-01-14 13:03:04] INFO: Computing consensus\n[2025-01-14 13:03:05] INFO: Alignment error rate: 0.175120\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/43/tmp/pymp-c5kjtoiw'\n[2025-01-14 13:03:05] INFO: >>>STAGE: repeat\n[2025-01-14 13:03:05] INFO: Building and resolving repeat graph\n[2025-01-14 13:03:05] INFO: Parsing disjointigs\n[2025-01-14 13:03:05] INFO: Building repeat graph\n0% 100% \n[2025-01-14 13:03:05] INFO: Median overlap divergence: 0.0151003\n[2025-01-14 13:03:05] INFO: Parsing reads\n[2025-01-14 13:03:05] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:03:05] INFO: Aligned read sequence: 1166207 / 1313105 (0.888129)\n[2025-01-14 13:03:05] INFO: Median overlap divergence: 0.0550349\n[2025-01-14 13:03:05] INFO: Mean edge coverage: 33\n[2025-01-14 13:03:05] INFO: Simplifying the graph\n[2025-01-14 13:03:05] INFO: >>>STAGE: contigger\n[2025-01-14 13:03:05] INFO: Generating contigs\n[2025-01-14 13:03:05] INFO: Reading sequences\n[2025-01-14 13:03:05] INFO: Generated 3 contigs\n[2025-01-14 13:03:05] INFO: Added 0 scaffold connections\n[2025-01-14 13:03:05] INFO: >>>STAGE: finalize\n[2025-01-14 13:03:05] INFO: Assembly statistics:\n\n\tTotal length:\t34929\n\tFragments:\t3\n\tFragments N50:\t21816\n\tLargest frg:\t21816\n\tScaffolds:\t0\n\tMean coverage:\t34\n\n[2025-01-14 13:03:05] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/43/working/out_dir/assembly.fasta\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:02:00", "plugin": "core", "name": "start_epoch", "raw_value": "1736859720.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:03:05", "plugin": "core", "name": "end_epoch", "raw_value": "1736859785.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "65.0000000"}]}, "status": "success"}}, {"id": "flye/2.9.5+galaxy0-2", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.9.5+galaxy0", "test_index": 2, "time_seconds": 20.392886877059937, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "flye/2.9.5+galaxy0-3", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.9.5+galaxy0", "test_index": 3, "time_seconds": 133.84715914726257, "inputs": {"inputs": [{"src": "hda", "id": "00207a43e076d177"}, {"src": "hda", "id": "14c4ea1c49f48023"}, {"src": "hda", "id": "3b58431cc5ce9dbf"}, {"src": "hda", "id": "f76aed4434d47657"}, {"src": "hda", "id": "db3d0389069a4a92"}, {"src": "hda", "id": "11d29caff3545e03"}, {"src": "hda", "id": "b1984d78df7cd1a1"}], "mode_conditional|mode": "--pacbio-raw", "meta": true}, "job": {"model_class": "Job", "id": "00207a43e076d177", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:05:48.906517", "create_time": "2025-01-14T13:04:18.553052", "galaxy_version": "23.1", "command_version": "2.9.5-b1801", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-f7tgc", "command_line": "ln -sf '/galaxy/server/database/objects/8/f/9/dataset_8f9da4cf-84dc-4131-9859-e7532403b981.dat' ./input_0.fastq.gz && ln -sf '/galaxy/server/database/objects/2/5/9/dataset_2590d770-b375-4729-9412-80abc07dcd9e.dat' ./input_1.fastq.gz && ln -sf '/galaxy/server/database/objects/8/a/3/dataset_8a3e98f7-27a9-4c80-be6d-c22fc45b33d6.dat' ./input_2.fastq.gz && ln -sf '/galaxy/server/database/objects/8/e/0/dataset_8e063f0f-ba8d-4b06-b8ae-9d001735a59a.dat' ./input_3.fastq.gz && ln -sf '/galaxy/server/database/objects/9/e/8/dataset_9e897cfa-0b21-4fea-a8ba-479928e759b7.dat' ./input_4.fastq.gz && ln -sf '/galaxy/server/database/objects/b/4/6/dataset_b465615e-9706-44b0-9d9a-ecde974bd095.dat' ./input_5.fastq.gz && ln -sf '/galaxy/server/database/objects/c/d/e/dataset_cdebf41d-b4dc-4642-b2e1-fb06af5d8ce4.dat' ./input_6.fastq.gz && flye --pacbio-raw ./input_0.fastq.gz ./input_1.fastq.gz ./input_2.fastq.gz ./input_3.fastq.gz ./input_4.fastq.gz ./input_5.fastq.gz ./input_6.fastq.gz -o out_dir -t ${GALAXY_SLOTS:-4} -i 1 --meta", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "generate_log": "false", "no_alt_contigs": "false", "asm": "{\"__current_case__\": 1, \"asm_select\": \"false\"}", "meta": "true", "scaffold": "false", "keep_haplotypes": "false", "min_overlap": "\"\"", "iterations": "\"1\"", "mode_conditional": "{\"__current_case__\": 3, \"mode\": \"--pacbio-raw\"}"}, "inputs": {"inputs": {"id": "00207a43e076d177", "src": "hda", "uuid": "8f9da4cf-84dc-4131-9859-e7532403b981"}, "inputs1": {"id": "00207a43e076d177", "src": "hda", "uuid": "8f9da4cf-84dc-4131-9859-e7532403b981"}, "inputs2": {"id": "14c4ea1c49f48023", "src": "hda", "uuid": "2590d770-b375-4729-9412-80abc07dcd9e"}, "inputs3": {"id": "3b58431cc5ce9dbf", "src": "hda", "uuid": "8a3e98f7-27a9-4c80-be6d-c22fc45b33d6"}, "inputs4": {"id": "f76aed4434d47657", "src": "hda", "uuid": "8e063f0f-ba8d-4b06-b8ae-9d001735a59a"}, "inputs5": {"id": "db3d0389069a4a92", "src": "hda", "uuid": "9e897cfa-0b21-4fea-a8ba-479928e759b7"}, "inputs6": {"id": "11d29caff3545e03", "src": "hda", "uuid": "b465615e-9706-44b0-9d9a-ecde974bd095"}, "inputs7": {"id": "b1984d78df7cd1a1", "src": "hda", "uuid": "cdebf41d-b4dc-4642-b2e1-fb06af5d8ce4"}}, "outputs": {"consensus": {"id": "ff7a67a99acd6eec", "src": "hda", "uuid": "184b6038-8dfd-4879-ba25-a9f9db2539d1"}, "assembly_graph": {"id": "d5ad4e094d2b6deb", "src": "hda", "uuid": "07694264-0e1e-4ad6-b7ce-a155a73de14c"}, "assembly_gfa": {"id": "858ba1a1ec62c394", "src": "hda", "uuid": "3cff7d0d-9dff-4c7b-a1ef-89ea80dce481"}, "assembly_info": {"id": "94f6cf1c03da6b8b", "src": "hda", "uuid": "aadcb949-dac0-4ba6-ab44-45136eb4d845"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[2025-01-14 13:04:21] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:04:21] INFO: >>>STAGE: configure\n[2025-01-14 13:04:21] INFO: Configuring run\n[2025-01-14 13:04:21] INFO: Total read length: 7249289\n[2025-01-14 13:04:21] INFO: Reads N50/N90: 11150 / 5790\n[2025-01-14 13:04:21] INFO: Minimum overlap set to 6000\n[2025-01-14 13:04:21] INFO: >>>STAGE: assembly\n[2025-01-14 13:04:21] INFO: Assembling disjointigs\n[2025-01-14 13:04:21] INFO: Reading sequences\n[2025-01-14 13:04:25] INFO: Counting k-mers:\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:05:15] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:05:16] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:05:18] INFO: Extending reads\n[2025-01-14 13:05:21] INFO: Overlap-based coverage: 10\n[2025-01-14 13:05:21] INFO: Median overlap divergence: 0.235584\n0% 80% 100% \n[2025-01-14 13:05:21] INFO: Assembled 1 disjointigs\n[2025-01-14 13:05:21] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:05:21] INFO: Filtering contained disjointigs\n0% 100% \n[2025-01-14 13:05:22] INFO: Contained seqs: 0\n[2025-01-14 13:05:22] INFO: >>>STAGE: consensus\n[2025-01-14 13:05:22] INFO: Running Minimap2\n[2025-01-14 13:05:23] INFO: Computing consensus\n[2025-01-14 13:05:28] INFO: Alignment error rate: 0.195502\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/60/tmp/pymp-ljk24ic5'\n[2025-01-14 13:05:28] INFO: >>>STAGE: repeat\n[2025-01-14 13:05:28] INFO: Building and resolving repeat graph\n[2025-01-14 13:05:28] INFO: Parsing disjointigs\n[2025-01-14 13:05:28] INFO: Building repeat graph\n0% 100% \n[2025-01-14 13:05:29] INFO: Median overlap divergence: 0\n[2025-01-14 13:05:29] INFO: Parsing reads\n[2025-01-14 13:05:29] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:05:30] INFO: Aligned read sequence: 6338340 / 6471580 (0.979412)\n[2025-01-14 13:05:30] INFO: Median overlap divergence: 0.129526\n[2025-01-14 13:05:30] INFO: Mean edge coverage: 14\n[2025-01-14 13:05:30] INFO: Simplifying the graph\n[2025-01-14 13:05:30] INFO: >>>STAGE: contigger\n[2025-01-14 13:05:30] INFO: Generating contigs\n[2025-01-14 13:05:30] INFO: Reading sequences\n[2025-01-14 13:05:30] INFO: Generated 1 contigs\n[2025-01-14 13:05:30] INFO: Added 0 scaffold connections\n[2025-01-14 13:05:30] INFO: >>>STAGE: polishing\n[2025-01-14 13:05:30] INFO: Polishing genome (1/1)\n[2025-01-14 13:05:30] INFO: Running minimap2\n[2025-01-14 13:05:31] INFO: Separating alignment into bubbles\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/60/tmp/pymp-d5lx4ut5'\n[2025-01-14 13:05:36] INFO: Alignment error rate: 0.126605\n[2025-01-14 13:05:36] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/60/tmp/pymp-wh3nas6o'\n[2025-01-14 13:05:40] INFO: >>>STAGE: finalize\n[2025-01-14 13:05:40] INFO: Assembly statistics:\n\n\tTotal length:\t418049\n\tFragments:\t1\n\tFragments N50:\t418049\n\tLargest frg:\t418049\n\tScaffolds:\t0\n\tMean coverage:\t17\n\n[2025-01-14 13:05:40] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/60/working/out_dir/assembly.fasta\n", "job_stdout": "", "job_stderr": "", "stderr": "[2025-01-14 13:04:21] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:04:21] INFO: >>>STAGE: configure\n[2025-01-14 13:04:21] INFO: Configuring run\n[2025-01-14 13:04:21] INFO: Total read length: 7249289\n[2025-01-14 13:04:21] INFO: Reads N50/N90: 11150 / 5790\n[2025-01-14 13:04:21] INFO: Minimum overlap set to 6000\n[2025-01-14 13:04:21] INFO: >>>STAGE: assembly\n[2025-01-14 13:04:21] INFO: Assembling disjointigs\n[2025-01-14 13:04:21] INFO: Reading sequences\n[2025-01-14 13:04:25] INFO: Counting k-mers:\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:05:15] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:05:16] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:05:18] INFO: Extending reads\n[2025-01-14 13:05:21] INFO: Overlap-based coverage: 10\n[2025-01-14 13:05:21] INFO: Median overlap divergence: 0.235584\n0% 80% 100% \n[2025-01-14 13:05:21] INFO: Assembled 1 disjointigs\n[2025-01-14 13:05:21] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:05:21] INFO: Filtering contained disjointigs\n0% 100% \n[2025-01-14 13:05:22] INFO: Contained seqs: 0\n[2025-01-14 13:05:22] INFO: >>>STAGE: consensus\n[2025-01-14 13:05:22] INFO: Running Minimap2\n[2025-01-14 13:05:23] INFO: Computing consensus\n[2025-01-14 13:05:28] INFO: Alignment error rate: 0.195502\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/60/tmp/pymp-ljk24ic5'\n[2025-01-14 13:05:28] INFO: >>>STAGE: repeat\n[2025-01-14 13:05:28] INFO: Building and resolving repeat graph\n[2025-01-14 13:05:28] INFO: Parsing disjointigs\n[2025-01-14 13:05:28] INFO: Building repeat graph\n0% 100% \n[2025-01-14 13:05:29] INFO: Median overlap divergence: 0\n[2025-01-14 13:05:29] INFO: Parsing reads\n[2025-01-14 13:05:29] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:05:30] INFO: Aligned read sequence: 6338340 / 6471580 (0.979412)\n[2025-01-14 13:05:30] INFO: Median overlap divergence: 0.129526\n[2025-01-14 13:05:30] INFO: Mean edge coverage: 14\n[2025-01-14 13:05:30] INFO: Simplifying the graph\n[2025-01-14 13:05:30] INFO: >>>STAGE: contigger\n[2025-01-14 13:05:30] INFO: Generating contigs\n[2025-01-14 13:05:30] INFO: Reading sequences\n[2025-01-14 13:05:30] INFO: Generated 1 contigs\n[2025-01-14 13:05:30] INFO: Added 0 scaffold connections\n[2025-01-14 13:05:30] INFO: >>>STAGE: polishing\n[2025-01-14 13:05:30] INFO: Polishing genome (1/1)\n[2025-01-14 13:05:30] INFO: Running minimap2\n[2025-01-14 13:05:31] INFO: Separating alignment into bubbles\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/60/tmp/pymp-d5lx4ut5'\n[2025-01-14 13:05:36] INFO: Alignment error rate: 0.126605\n[2025-01-14 13:05:36] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/60/tmp/pymp-wh3nas6o'\n[2025-01-14 13:05:40] INFO: >>>STAGE: finalize\n[2025-01-14 13:05:40] INFO: Assembly statistics:\n\n\tTotal length:\t418049\n\tFragments:\t1\n\tFragments N50:\t418049\n\tLargest frg:\t418049\n\tScaffolds:\t0\n\tMean coverage:\t17\n\n[2025-01-14 13:05:40] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/60/working/out_dir/assembly.fasta\n", "stdout": "", "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": "80.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:05:40", "plugin": "core", "name": "end_epoch", "raw_value": "1736859940.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:04:20", "plugin": "core", "name": "start_epoch", "raw_value": "1736859860.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "output_problems": ["Output assembly_gfa: different than expected\nExpected file size of 418729+-100 found 418099", "Output consensus: different than expected\nExpected file size of 425667+-100 found 425027"], "status": "failure"}}, {"id": "flye/2.9.5+galaxy0-4", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.9.5+galaxy0", "test_index": 4, "time_seconds": 63.029197216033936, "inputs": {"inputs": [{"src": "hda", "id": "be2291bd8c303b28"}, {"src": "hda", "id": "676ab4c198e41c95"}, {"src": "hda", "id": "f321b7d90e985353"}, {"src": "hda", "id": "c07d3e3bbdee4a24"}, {"src": "hda", "id": "df9a62ff618318ca"}, {"src": "hda", "id": "2c9d48d14126612d"}, {"src": "hda", "id": "a88123db56730dda"}, {"src": "hda", "id": "434a162dc68c32e5"}, {"src": "hda", "id": "cfe8361ef3e799e6"}], "mode_conditional|mode": "--nano-hq", "min_overlap": "1000"}, "job": {"model_class": "Job", "id": "94f6cf1c03da6b8b", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:06:51.139649", "create_time": "2025-01-14T13:06:29.955196", "galaxy_version": "23.1", "command_version": "2.9.5-b1801", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-cjmp4", "command_line": "ln -sf '/galaxy/server/database/objects/3/3/8/dataset_3388701c-2934-43ce-a8ad-75aa00d0e1c3.dat' ./input_0.fastq.gz && ln -sf '/galaxy/server/database/objects/f/b/9/dataset_fb9ad18d-9772-4d9d-a562-566fb73d0f55.dat' ./input_1.fastq.gz && ln -sf '/galaxy/server/database/objects/6/f/0/dataset_6f065b8d-e8c6-41b4-95d1-7ea2c5a5d516.dat' ./input_2.fastq.gz && ln -sf '/galaxy/server/database/objects/a/a/2/dataset_aa235817-e1cd-482b-bbfa-7a2745086c2e.dat' ./input_3.fastq.gz && ln -sf '/galaxy/server/database/objects/8/3/5/dataset_835f3eb8-361d-49a2-bd5e-3a767b0b12d1.dat' ./input_4.fastq.gz && ln -sf '/galaxy/server/database/objects/2/0/c/dataset_20c39362-f884-4b11-8666-b145159032d5.dat' ./input_5.fastq.gz && ln -sf '/galaxy/server/database/objects/5/d/3/dataset_5d391c2a-85bd-4e09-916b-0e1b22eb7916.dat' ./input_6.fastq.gz && ln -sf '/galaxy/server/database/objects/0/0/2/dataset_002baba2-2ba4-4ed0-b428-d3d2e4173f81.dat' ./input_7.fastq.gz && ln -sf '/galaxy/server/database/objects/5/b/8/dataset_5b8d3bc6-8ca2-4091-9ebc-ec34b9780f02.dat' ./input_8.fastq.gz && flye --nano-hq ./input_0.fastq.gz ./input_1.fastq.gz ./input_2.fastq.gz ./input_3.fastq.gz ./input_4.fastq.gz ./input_5.fastq.gz ./input_6.fastq.gz ./input_7.fastq.gz ./input_8.fastq.gz -o out_dir -t ${GALAXY_SLOTS:-4} -i 1 -m 1000", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "generate_log": "false", "no_alt_contigs": "false", "asm": "{\"__current_case__\": 1, \"asm_select\": \"false\"}", "meta": "false", "scaffold": "false", "keep_haplotypes": "false", "min_overlap": "\"1000\"", "iterations": "\"1\"", "mode_conditional": "{\"__current_case__\": 2, \"mode\": \"--nano-hq\"}"}, "inputs": {"inputs": {"id": "be2291bd8c303b28", "src": "hda", "uuid": "3388701c-2934-43ce-a8ad-75aa00d0e1c3"}, "inputs1": {"id": "be2291bd8c303b28", "src": "hda", "uuid": "3388701c-2934-43ce-a8ad-75aa00d0e1c3"}, "inputs2": {"id": "676ab4c198e41c95", "src": "hda", "uuid": "fb9ad18d-9772-4d9d-a562-566fb73d0f55"}, "inputs3": {"id": "f321b7d90e985353", "src": "hda", "uuid": "6f065b8d-e8c6-41b4-95d1-7ea2c5a5d516"}, "inputs4": {"id": "c07d3e3bbdee4a24", "src": "hda", "uuid": "aa235817-e1cd-482b-bbfa-7a2745086c2e"}, "inputs5": {"id": "df9a62ff618318ca", "src": "hda", "uuid": "835f3eb8-361d-49a2-bd5e-3a767b0b12d1"}, "inputs6": {"id": "2c9d48d14126612d", "src": "hda", "uuid": "20c39362-f884-4b11-8666-b145159032d5"}, "inputs7": {"id": "a88123db56730dda", "src": "hda", "uuid": "5d391c2a-85bd-4e09-916b-0e1b22eb7916"}, "inputs8": {"id": "434a162dc68c32e5", "src": "hda", "uuid": "002baba2-2ba4-4ed0-b428-d3d2e4173f81"}, "inputs9": {"id": "cfe8361ef3e799e6", "src": "hda", "uuid": "5b8d3bc6-8ca2-4091-9ebc-ec34b9780f02"}}, "outputs": {"consensus": {"id": "4c7e3f38f8921172", "src": "hda", "uuid": "2dfb9287-3ff8-41a5-8e67-1e1aa6fc718a"}, "assembly_graph": {"id": "4035217a70da49ac", "src": "hda", "uuid": "ef7be25a-8cff-490f-963a-7f331ae337d2"}, "assembly_gfa": {"id": "d6eaf2d2cb5cf012", "src": "hda", "uuid": "6914e198-3304-469e-9ab1-9de227e96d37"}, "assembly_info": {"id": "5ab52f6b4ba75962", "src": "hda", "uuid": "424f00ed-bc08-4a95-8d27-78691c8960d3"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[2025-01-14 13:06:31] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:06:31] INFO: >>>STAGE: configure\n[2025-01-14 13:06:31] INFO: Configuring run\n[2025-01-14 13:06:31] INFO: Total read length: 6522170\n[2025-01-14 13:06:31] INFO: Reads N50/N90: 2706 / 1386\n[2025-01-14 13:06:31] INFO: Selected minimum overlap: 1000\n[2025-01-14 13:06:31] INFO: >>>STAGE: assembly\n[2025-01-14 13:06:31] INFO: Assembling disjointigs\n[2025-01-14 13:06:31] INFO: Reading sequences\n[2025-01-14 13:06:31] INFO: Building minimizer index\n[2025-01-14 13:06:31] INFO: Pre-calculating index storage\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:32] INFO: Filling index\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:32] INFO: Extending reads\n[2025-01-14 13:06:35] INFO: Overlap-based coverage: 12\n[2025-01-14 13:06:35] INFO: Median overlap divergence: 0.0135674\n0% 10% 20% 30% 40% 60% 80% 90% 100% \n[2025-01-14 13:06:35] INFO: Assembled 10 disjointigs\n[2025-01-14 13:06:35] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:35] INFO: Filtering contained disjointigs\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:35] INFO: Contained seqs: 0\n[2025-01-14 13:06:35] INFO: >>>STAGE: consensus\n[2025-01-14 13:06:35] INFO: Running Minimap2\n[2025-01-14 13:06:36] INFO: Computing consensus\n[2025-01-14 13:06:37] INFO: Alignment error rate: 0.018062\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/70/tmp/pymp-_jfywtgl'\n[2025-01-14 13:06:37] INFO: >>>STAGE: repeat\n[2025-01-14 13:06:37] INFO: Building and resolving repeat graph\n[2025-01-14 13:06:37] INFO: Parsing disjointigs\n[2025-01-14 13:06:37] INFO: Building repeat graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:37] INFO: Median overlap divergence: 0.00146056\n[2025-01-14 13:06:37] INFO: Parsing reads\n[2025-01-14 13:06:37] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:38] INFO: Aligned read sequence: 6385160 / 6522170 (0.978993)\n[2025-01-14 13:06:38] INFO: Median overlap divergence: 0.00691777\n[2025-01-14 13:06:38] INFO: Mean edge coverage: 14\n[2025-01-14 13:06:38] INFO: Simplifying the graph\n[2025-01-14 13:06:38] INFO: >>>STAGE: contigger\n[2025-01-14 13:06:38] INFO: Generating contigs\n[2025-01-14 13:06:38] INFO: Reading sequences\n[2025-01-14 13:06:38] INFO: Generated 4 contigs\n[2025-01-14 13:06:38] INFO: Added 0 scaffold connections\n[2025-01-14 13:06:38] INFO: >>>STAGE: polishing\n[2025-01-14 13:06:38] INFO: Polishing genome (1/1)\n[2025-01-14 13:06:38] INFO: Running minimap2\n[2025-01-14 13:06:38] INFO: Separating alignment into bubbles\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/70/tmp/pymp-qrfceht3'\n[2025-01-14 13:06:40] INFO: Alignment error rate: 0.010378\n[2025-01-14 13:06:40] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/70/tmp/pymp-bh0w3wrf'\n[2025-01-14 13:06:42] INFO: >>>STAGE: finalize\n[2025-01-14 13:06:42] INFO: Assembly statistics:\n\n\tTotal length:\t419248\n\tFragments:\t4\n\tFragments N50:\t147965\n\tLargest frg:\t150253\n\tScaffolds:\t0\n\tMean coverage:\t16\n\n[2025-01-14 13:06:42] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/70/working/out_dir/assembly.fasta\n", "job_stdout": "", "job_stderr": "", "stderr": "[2025-01-14 13:06:31] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:06:31] INFO: >>>STAGE: configure\n[2025-01-14 13:06:31] INFO: Configuring run\n[2025-01-14 13:06:31] INFO: Total read length: 6522170\n[2025-01-14 13:06:31] INFO: Reads N50/N90: 2706 / 1386\n[2025-01-14 13:06:31] INFO: Selected minimum overlap: 1000\n[2025-01-14 13:06:31] INFO: >>>STAGE: assembly\n[2025-01-14 13:06:31] INFO: Assembling disjointigs\n[2025-01-14 13:06:31] INFO: Reading sequences\n[2025-01-14 13:06:31] INFO: Building minimizer index\n[2025-01-14 13:06:31] INFO: Pre-calculating index storage\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:32] INFO: Filling index\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:32] INFO: Extending reads\n[2025-01-14 13:06:35] INFO: Overlap-based coverage: 12\n[2025-01-14 13:06:35] INFO: Median overlap divergence: 0.0135674\n0% 10% 20% 30% 40% 60% 80% 90% 100% \n[2025-01-14 13:06:35] INFO: Assembled 10 disjointigs\n[2025-01-14 13:06:35] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:35] INFO: Filtering contained disjointigs\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:35] INFO: Contained seqs: 0\n[2025-01-14 13:06:35] INFO: >>>STAGE: consensus\n[2025-01-14 13:06:35] INFO: Running Minimap2\n[2025-01-14 13:06:36] INFO: Computing consensus\n[2025-01-14 13:06:37] INFO: Alignment error rate: 0.018062\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/70/tmp/pymp-_jfywtgl'\n[2025-01-14 13:06:37] INFO: >>>STAGE: repeat\n[2025-01-14 13:06:37] INFO: Building and resolving repeat graph\n[2025-01-14 13:06:37] INFO: Parsing disjointigs\n[2025-01-14 13:06:37] INFO: Building repeat graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:37] INFO: Median overlap divergence: 0.00146056\n[2025-01-14 13:06:37] INFO: Parsing reads\n[2025-01-14 13:06:37] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:06:38] INFO: Aligned read sequence: 6385160 / 6522170 (0.978993)\n[2025-01-14 13:06:38] INFO: Median overlap divergence: 0.00691777\n[2025-01-14 13:06:38] INFO: Mean edge coverage: 14\n[2025-01-14 13:06:38] INFO: Simplifying the graph\n[2025-01-14 13:06:38] INFO: >>>STAGE: contigger\n[2025-01-14 13:06:38] INFO: Generating contigs\n[2025-01-14 13:06:38] INFO: Reading sequences\n[2025-01-14 13:06:38] INFO: Generated 4 contigs\n[2025-01-14 13:06:38] INFO: Added 0 scaffold connections\n[2025-01-14 13:06:38] INFO: >>>STAGE: polishing\n[2025-01-14 13:06:38] INFO: Polishing genome (1/1)\n[2025-01-14 13:06:38] INFO: Running minimap2\n[2025-01-14 13:06:38] INFO: Separating alignment into bubbles\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/70/tmp/pymp-qrfceht3'\n[2025-01-14 13:06:40] INFO: Alignment error rate: 0.010378\n[2025-01-14 13:06:40] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/70/tmp/pymp-bh0w3wrf'\n[2025-01-14 13:06:42] INFO: >>>STAGE: finalize\n[2025-01-14 13:06:42] INFO: Assembly statistics:\n\n\tTotal length:\t419248\n\tFragments:\t4\n\tFragments N50:\t147965\n\tLargest frg:\t150253\n\tScaffolds:\t0\n\tMean coverage:\t16\n\n[2025-01-14 13:06:42] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/70/working/out_dir/assembly.fasta\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "11 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "11.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:06:42", "plugin": "core", "name": "end_epoch", "raw_value": "1736860002.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:06:31", "plugin": "core", "name": "start_epoch", "raw_value": "1736859991.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "flye/2.9.5+galaxy0-5", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.9.5+galaxy0", "test_index": 5, "time_seconds": 68.83472895622253, "inputs": {"inputs": [{"src": "hda", "id": "f2dbe4d234632241"}, {"src": "hda", "id": "72de3d8512e96325"}, {"src": "hda", "id": "81dc4f6d51ba7b35"}, {"src": "hda", "id": "03c915b88c68de2a"}, {"src": "hda", "id": "72b19dd0e38577c6"}, {"src": "hda", "id": "365716201f6133f5"}, {"src": "hda", "id": "666e4c921fda6878"}, {"src": "hda", "id": "786ee2c45dfffdcb"}, {"src": "hda", "id": "e5b4f567d38f64e4"}], "mode_conditional|hifi_error": "0.21", "mode_conditional|mode": "--pacbio-hifi", "min_overlap": "1000"}, "job": {"model_class": "Job", "id": "4c7e3f38f8921172", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:08:00.037959", "create_time": "2025-01-14T13:07:31.861310", "galaxy_version": "23.1", "command_version": "2.9.5-b1801", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-wv96w", "command_line": "ln -sf '/galaxy/server/database/objects/e/d/a/dataset_edac2636-bcde-4884-8610-cbca75d2f678.dat' ./input_0.fastq.gz && ln -sf '/galaxy/server/database/objects/1/a/8/dataset_1a8309b0-0a4a-4ad3-bc42-e71bf2e707d5.dat' ./input_1.fastq.gz && ln -sf '/galaxy/server/database/objects/5/7/c/dataset_57c0dd86-affd-4377-8564-518e4bcdcb91.dat' ./input_2.fastq.gz && ln -sf '/galaxy/server/database/objects/f/8/6/dataset_f86dc189-3fc3-42ee-8aaa-249525d543b2.dat' ./input_3.fastq.gz && ln -sf '/galaxy/server/database/objects/5/2/c/dataset_52cb31b4-5c75-4e07-aead-cdf2dcbae5ab.dat' ./input_4.fastq.gz && ln -sf '/galaxy/server/database/objects/a/3/3/dataset_a33b506e-2827-4019-b226-fc422c4cc7fb.dat' ./input_5.fastq.gz && ln -sf '/galaxy/server/database/objects/4/f/8/dataset_4f8550d4-2e4b-47c7-9729-0fc2dfdf3f84.dat' ./input_6.fastq.gz && ln -sf '/galaxy/server/database/objects/d/9/b/dataset_d9be2582-a460-4803-ab7b-a2c3438ce3bd.dat' ./input_7.fastq.gz && ln -sf '/galaxy/server/database/objects/e/1/f/dataset_e1fbbbd0-532f-474b-abcb-64958c7b7aaa.dat' ./input_8.fastq.gz && flye --pacbio-hifi ./input_0.fastq.gz ./input_1.fastq.gz ./input_2.fastq.gz ./input_3.fastq.gz ./input_4.fastq.gz ./input_5.fastq.gz ./input_6.fastq.gz ./input_7.fastq.gz ./input_8.fastq.gz -o out_dir -t ${GALAXY_SLOTS:-4} -i 1 --hifi-error 0.21 -m 1000", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "generate_log": "false", "no_alt_contigs": "false", "asm": "{\"__current_case__\": 1, \"asm_select\": \"false\"}", "meta": "false", "scaffold": "false", "keep_haplotypes": "false", "min_overlap": "\"1000\"", "iterations": "\"1\"", "mode_conditional": "{\"__current_case__\": 5, \"hifi_error\": \"0.21\", \"mode\": \"--pacbio-hifi\"}"}, "inputs": {"inputs": {"id": "f2dbe4d234632241", "src": "hda", "uuid": "edac2636-bcde-4884-8610-cbca75d2f678"}, "inputs1": {"id": "f2dbe4d234632241", "src": "hda", "uuid": "edac2636-bcde-4884-8610-cbca75d2f678"}, "inputs2": {"id": "72de3d8512e96325", "src": "hda", "uuid": "1a8309b0-0a4a-4ad3-bc42-e71bf2e707d5"}, "inputs3": {"id": "81dc4f6d51ba7b35", "src": "hda", "uuid": "57c0dd86-affd-4377-8564-518e4bcdcb91"}, "inputs4": {"id": "03c915b88c68de2a", "src": "hda", "uuid": "f86dc189-3fc3-42ee-8aaa-249525d543b2"}, "inputs5": {"id": "72b19dd0e38577c6", "src": "hda", "uuid": "52cb31b4-5c75-4e07-aead-cdf2dcbae5ab"}, "inputs6": {"id": "365716201f6133f5", "src": "hda", "uuid": "a33b506e-2827-4019-b226-fc422c4cc7fb"}, "inputs7": {"id": "666e4c921fda6878", "src": "hda", "uuid": "4f8550d4-2e4b-47c7-9729-0fc2dfdf3f84"}, "inputs8": {"id": "786ee2c45dfffdcb", "src": "hda", "uuid": "d9be2582-a460-4803-ab7b-a2c3438ce3bd"}, "inputs9": {"id": "e5b4f567d38f64e4", "src": "hda", "uuid": "e1fbbbd0-532f-474b-abcb-64958c7b7aaa"}}, "outputs": {"consensus": {"id": "8ee04393e2c6d9a9", "src": "hda", "uuid": "3f61ebd0-60c6-491d-8643-684604ad6606"}, "assembly_graph": {"id": "b0b9afd458eb5094", "src": "hda", "uuid": "64ce6e11-5666-421f-a883-3058aa9c1588"}, "assembly_gfa": {"id": "c9c26d406d582773", "src": "hda", "uuid": "de6ff8be-301d-4ed2-b54e-f0de1f87d701"}, "assembly_info": {"id": "a86ab55b15a5f26d", "src": "hda", "uuid": "b35225db-a2b2-4b0e-a99e-abd8248686f1"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[2025-01-14 13:07:34] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:07:34] INFO: >>>STAGE: configure\n[2025-01-14 13:07:34] INFO: Configuring run\n[2025-01-14 13:07:34] INFO: Total read length: 6522170\n[2025-01-14 13:07:34] INFO: Reads N50/N90: 2706 / 1386\n[2025-01-14 13:07:34] INFO: Selected minimum overlap: 1000\n[2025-01-14 13:07:34] INFO: >>>STAGE: assembly\n[2025-01-14 13:07:34] INFO: Assembling disjointigs\n[2025-01-14 13:07:34] INFO: Reading sequences\n[2025-01-14 13:07:35] INFO: Building minimizer index\n[2025-01-14 13:07:35] INFO: Pre-calculating index storage\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:35] INFO: Filling index\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:35] INFO: Extending reads\n[2025-01-14 13:07:38] INFO: Overlap-based coverage: 12\n[2025-01-14 13:07:38] INFO: Median overlap divergence: 0.0135674\n0% 10% 20% 30% 40% 60% 80% 90% 100% \n[2025-01-14 13:07:38] INFO: Assembled 12 disjointigs\n[2025-01-14 13:07:38] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:38] INFO: Filtering contained disjointigs\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:38] INFO: Contained seqs: 0\n[2025-01-14 13:07:38] INFO: >>>STAGE: consensus\n[2025-01-14 13:07:38] INFO: Running Minimap2\n[2025-01-14 13:07:39] INFO: Computing consensus\n[2025-01-14 13:07:40] INFO: Alignment error rate: 0.018150\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/80/tmp/pymp-pnh8pejn'\n[2025-01-14 13:07:40] INFO: >>>STAGE: repeat\n[2025-01-14 13:07:40] INFO: Building and resolving repeat graph\n[2025-01-14 13:07:40] INFO: Parsing disjointigs\n[2025-01-14 13:07:40] INFO: Building repeat graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:40] INFO: Median overlap divergence: 0.00293725\n[2025-01-14 13:07:40] INFO: Parsing reads\n[2025-01-14 13:07:40] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:41] INFO: Aligned read sequence: 6400847 / 6522170 (0.981398)\n[2025-01-14 13:07:41] INFO: Median overlap divergence: 0.00690788\n[2025-01-14 13:07:41] INFO: Mean edge coverage: 14\n[2025-01-14 13:07:41] INFO: Simplifying the graph\n[2025-01-14 13:07:41] INFO: >>>STAGE: contigger\n[2025-01-14 13:07:41] INFO: Generating contigs\n[2025-01-14 13:07:41] INFO: Reading sequences\n[2025-01-14 13:07:41] INFO: Generated 5 contigs\n[2025-01-14 13:07:41] INFO: Added 0 scaffold connections\n[2025-01-14 13:07:41] INFO: >>>STAGE: polishing\n[2025-01-14 13:07:41] INFO: Polishing genome (1/1)\n[2025-01-14 13:07:41] INFO: Running minimap2\n[2025-01-14 13:07:42] INFO: Separating alignment into bubbles\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/80/tmp/pymp-e8n043xf'\n[2025-01-14 13:07:43] INFO: Alignment error rate: 0.009940\n[2025-01-14 13:07:43] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/80/tmp/pymp-yuvrjvx1'\n[2025-01-14 13:07:50] INFO: >>>STAGE: finalize\n[2025-01-14 13:07:50] INFO: Assembly statistics:\n\n\tTotal length:\t418250\n\tFragments:\t5\n\tFragments N50:\t90295\n\tLargest frg:\t147965\n\tScaffolds:\t0\n\tMean coverage:\t16\n\n[2025-01-14 13:07:50] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/80/working/out_dir/assembly.fasta\n", "job_stdout": "", "job_stderr": "", "stderr": "[2025-01-14 13:07:34] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:07:34] INFO: >>>STAGE: configure\n[2025-01-14 13:07:34] INFO: Configuring run\n[2025-01-14 13:07:34] INFO: Total read length: 6522170\n[2025-01-14 13:07:34] INFO: Reads N50/N90: 2706 / 1386\n[2025-01-14 13:07:34] INFO: Selected minimum overlap: 1000\n[2025-01-14 13:07:34] INFO: >>>STAGE: assembly\n[2025-01-14 13:07:34] INFO: Assembling disjointigs\n[2025-01-14 13:07:34] INFO: Reading sequences\n[2025-01-14 13:07:35] INFO: Building minimizer index\n[2025-01-14 13:07:35] INFO: Pre-calculating index storage\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:35] INFO: Filling index\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:35] INFO: Extending reads\n[2025-01-14 13:07:38] INFO: Overlap-based coverage: 12\n[2025-01-14 13:07:38] INFO: Median overlap divergence: 0.0135674\n0% 10% 20% 30% 40% 60% 80% 90% 100% \n[2025-01-14 13:07:38] INFO: Assembled 12 disjointigs\n[2025-01-14 13:07:38] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:38] INFO: Filtering contained disjointigs\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:38] INFO: Contained seqs: 0\n[2025-01-14 13:07:38] INFO: >>>STAGE: consensus\n[2025-01-14 13:07:38] INFO: Running Minimap2\n[2025-01-14 13:07:39] INFO: Computing consensus\n[2025-01-14 13:07:40] INFO: Alignment error rate: 0.018150\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/80/tmp/pymp-pnh8pejn'\n[2025-01-14 13:07:40] INFO: >>>STAGE: repeat\n[2025-01-14 13:07:40] INFO: Building and resolving repeat graph\n[2025-01-14 13:07:40] INFO: Parsing disjointigs\n[2025-01-14 13:07:40] INFO: Building repeat graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:40] INFO: Median overlap divergence: 0.00293725\n[2025-01-14 13:07:40] INFO: Parsing reads\n[2025-01-14 13:07:40] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:07:41] INFO: Aligned read sequence: 6400847 / 6522170 (0.981398)\n[2025-01-14 13:07:41] INFO: Median overlap divergence: 0.00690788\n[2025-01-14 13:07:41] INFO: Mean edge coverage: 14\n[2025-01-14 13:07:41] INFO: Simplifying the graph\n[2025-01-14 13:07:41] INFO: >>>STAGE: contigger\n[2025-01-14 13:07:41] INFO: Generating contigs\n[2025-01-14 13:07:41] INFO: Reading sequences\n[2025-01-14 13:07:41] INFO: Generated 5 contigs\n[2025-01-14 13:07:41] INFO: Added 0 scaffold connections\n[2025-01-14 13:07:41] INFO: >>>STAGE: polishing\n[2025-01-14 13:07:41] INFO: Polishing genome (1/1)\n[2025-01-14 13:07:41] INFO: Running minimap2\n[2025-01-14 13:07:42] INFO: Separating alignment into bubbles\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/80/tmp/pymp-e8n043xf'\n[2025-01-14 13:07:43] INFO: Alignment error rate: 0.009940\n[2025-01-14 13:07:43] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/80/tmp/pymp-yuvrjvx1'\n[2025-01-14 13:07:50] INFO: >>>STAGE: finalize\n[2025-01-14 13:07:50] INFO: Assembly statistics:\n\n\tTotal length:\t418250\n\tFragments:\t5\n\tFragments N50:\t90295\n\tLargest frg:\t147965\n\tScaffolds:\t0\n\tMean coverage:\t16\n\n[2025-01-14 13:07:50] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/80/working/out_dir/assembly.fasta\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "16 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "16.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:07:50", "plugin": "core", "name": "end_epoch", "raw_value": "1736860070.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:07:34", "plugin": "core", "name": "start_epoch", "raw_value": "1736860054.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "flye/2.9.5+galaxy0-6", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.9.5+galaxy0", "test_index": 6, "time_seconds": 30.178921937942505, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "flye/2.9.5+galaxy0-7", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.9.5+galaxy0", "test_index": 7, "time_seconds": 64.72299337387085, "inputs": {"inputs": [{"src": "hda", "id": "945e3b79af9f8617"}, {"src": "hda", "id": "62492a51c4a525b5"}, {"src": "hda", "id": "eff0a467d2299c29"}, {"src": "hda", "id": "12177588ca8de124"}, {"src": "hda", "id": "eded755991c65dc6"}, {"src": "hda", "id": "3a0763d83dcbdec9"}, {"src": "hda", "id": "5edd4c03065df6aa"}, {"src": "hda", "id": "44ea39807d633a74"}, {"src": "hda", "id": "4dadee7e4b90857d"}], "mode_conditional|mode": "--nano-hq", "min_overlap": "1000", "scaffold": true}, "job": {"model_class": "Job", "id": "e7debf96a7e91232", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:09:35.326054", "create_time": "2025-01-14T13:09:13.643441", "galaxy_version": "23.1", "command_version": "2.9.5-b1801", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-964fz", "command_line": "ln -sf '/galaxy/server/database/objects/4/0/8/dataset_4081a238-2cbb-47bc-b7ab-40da5734b7a3.dat' ./input_0.fastq.gz && ln -sf '/galaxy/server/database/objects/a/9/8/dataset_a98e31d2-34a9-4595-a72d-c2aacb458a6d.dat' ./input_1.fastq.gz && ln -sf '/galaxy/server/database/objects/a/1/c/dataset_a1cea1fe-6aca-488b-97ba-523deba319c7.dat' ./input_2.fastq.gz && ln -sf '/galaxy/server/database/objects/2/6/4/dataset_264ea4aa-5ac6-455d-8aca-d09e68443bf9.dat' ./input_3.fastq.gz && ln -sf '/galaxy/server/database/objects/2/1/1/dataset_21129c2f-abaa-44be-9fb1-b2ae514d04f9.dat' ./input_4.fastq.gz && ln -sf '/galaxy/server/database/objects/2/5/4/dataset_25453e13-7a57-4673-bdfd-cdf8eaf66438.dat' ./input_5.fastq.gz && ln -sf '/galaxy/server/database/objects/1/5/d/dataset_15d459ff-414b-49b2-a866-a7744a14a734.dat' ./input_6.fastq.gz && ln -sf '/galaxy/server/database/objects/0/0/5/dataset_0055cd57-2d85-45b0-aa8e-7845c6892b0a.dat' ./input_7.fastq.gz && ln -sf '/galaxy/server/database/objects/4/9/2/dataset_49200f76-63f2-46a5-b834-d197f610f93e.dat' ./input_8.fastq.gz && flye --nano-hq ./input_0.fastq.gz ./input_1.fastq.gz ./input_2.fastq.gz ./input_3.fastq.gz ./input_4.fastq.gz ./input_5.fastq.gz ./input_6.fastq.gz ./input_7.fastq.gz ./input_8.fastq.gz -o out_dir -t ${GALAXY_SLOTS:-4} -i 1 -m 1000 --scaffold", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "generate_log": "false", "no_alt_contigs": "false", "asm": "{\"__current_case__\": 1, \"asm_select\": \"false\"}", "meta": "false", "scaffold": "true", "keep_haplotypes": "false", "min_overlap": "\"1000\"", "iterations": "\"1\"", "mode_conditional": "{\"__current_case__\": 2, \"mode\": \"--nano-hq\"}"}, "inputs": {"inputs": {"id": "945e3b79af9f8617", "src": "hda", "uuid": "4081a238-2cbb-47bc-b7ab-40da5734b7a3"}, "inputs1": {"id": "945e3b79af9f8617", "src": "hda", "uuid": "4081a238-2cbb-47bc-b7ab-40da5734b7a3"}, "inputs2": {"id": "62492a51c4a525b5", "src": "hda", "uuid": "a98e31d2-34a9-4595-a72d-c2aacb458a6d"}, "inputs3": {"id": "eff0a467d2299c29", "src": "hda", "uuid": "a1cea1fe-6aca-488b-97ba-523deba319c7"}, "inputs4": {"id": "12177588ca8de124", "src": "hda", "uuid": "264ea4aa-5ac6-455d-8aca-d09e68443bf9"}, "inputs5": {"id": "eded755991c65dc6", "src": "hda", "uuid": "21129c2f-abaa-44be-9fb1-b2ae514d04f9"}, "inputs6": {"id": "3a0763d83dcbdec9", "src": "hda", "uuid": "25453e13-7a57-4673-bdfd-cdf8eaf66438"}, "inputs7": {"id": "5edd4c03065df6aa", "src": "hda", "uuid": "15d459ff-414b-49b2-a866-a7744a14a734"}, "inputs8": {"id": "44ea39807d633a74", "src": "hda", "uuid": "0055cd57-2d85-45b0-aa8e-7845c6892b0a"}, "inputs9": {"id": "4dadee7e4b90857d", "src": "hda", "uuid": "49200f76-63f2-46a5-b834-d197f610f93e"}}, "outputs": {"consensus": {"id": "c975c3068600f661", "src": "hda", "uuid": "facfa951-0e25-418e-8fcc-6d1893ffe4cb"}, "assembly_graph": {"id": "0a89e92e47898649", "src": "hda", "uuid": "51df63a5-bdc3-43a1-b760-0ec38ab32c38"}, "assembly_gfa": {"id": "300a3677dbe0b047", "src": "hda", "uuid": "a6d6c509-a563-46f4-b7b2-7939e9c958a1"}, "assembly_info": {"id": "9a97793f0d9b0464", "src": "hda", "uuid": "4a0a8125-213c-4ece-993a-0d45bc8e22db"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[2025-01-14 13:09:15] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:09:15] INFO: >>>STAGE: configure\n[2025-01-14 13:09:15] INFO: Configuring run\n[2025-01-14 13:09:15] INFO: Total read length: 6522170\n[2025-01-14 13:09:15] INFO: Reads N50/N90: 2706 / 1386\n[2025-01-14 13:09:15] INFO: Selected minimum overlap: 1000\n[2025-01-14 13:09:15] INFO: >>>STAGE: assembly\n[2025-01-14 13:09:15] INFO: Assembling disjointigs\n[2025-01-14 13:09:15] INFO: Reading sequences\n[2025-01-14 13:09:15] INFO: Building minimizer index\n[2025-01-14 13:09:15] INFO: Pre-calculating index storage\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:16] INFO: Filling index\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:16] INFO: Extending reads\n[2025-01-14 13:09:19] INFO: Overlap-based coverage: 12\n[2025-01-14 13:09:19] INFO: Median overlap divergence: 0.0135674\n0% 10% 20% 30% 40% 70% 80% 90% 100% \n[2025-01-14 13:09:19] INFO: Assembled 11 disjointigs\n[2025-01-14 13:09:19] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:19] INFO: Filtering contained disjointigs\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:19] INFO: Contained seqs: 0\n[2025-01-14 13:09:19] INFO: >>>STAGE: consensus\n[2025-01-14 13:09:19] INFO: Running Minimap2\n[2025-01-14 13:09:20] INFO: Computing consensus\n[2025-01-14 13:09:21] INFO: Alignment error rate: 0.018082\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/99/tmp/pymp-n2s5mmme'\n[2025-01-14 13:09:21] INFO: >>>STAGE: repeat\n[2025-01-14 13:09:21] INFO: Building and resolving repeat graph\n[2025-01-14 13:09:21] INFO: Parsing disjointigs\n[2025-01-14 13:09:21] INFO: Building repeat graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:21] INFO: Median overlap divergence: 0.000980392\n[2025-01-14 13:09:21] INFO: Parsing reads\n[2025-01-14 13:09:21] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:22] INFO: Aligned read sequence: 6403986 / 6522170 (0.98188)\n[2025-01-14 13:09:22] INFO: Median overlap divergence: 0.00689656\n[2025-01-14 13:09:22] INFO: Mean edge coverage: 14\n[2025-01-14 13:09:22] INFO: Simplifying the graph\n[2025-01-14 13:09:22] INFO: >>>STAGE: contigger\n[2025-01-14 13:09:22] INFO: Generating contigs\n[2025-01-14 13:09:22] INFO: Reading sequences\n[2025-01-14 13:09:22] INFO: Generated 4 contigs\n[2025-01-14 13:09:22] INFO: Added 0 scaffold connections\n[2025-01-14 13:09:22] INFO: >>>STAGE: polishing\n[2025-01-14 13:09:22] INFO: Polishing genome (1/1)\n[2025-01-14 13:09:22] INFO: Running minimap2\n[2025-01-14 13:09:22] INFO: Separating alignment into bubbles\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/99/tmp/pymp-5kmiqtfe'\n[2025-01-14 13:09:24] INFO: Alignment error rate: 0.009628\n[2025-01-14 13:09:24] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/99/tmp/pymp-0620o1k5'\n[2025-01-14 13:09:26] INFO: >>>STAGE: finalize\n[2025-01-14 13:09:26] INFO: Assembly statistics:\n\n\tTotal length:\t419247\n\tFragments:\t4\n\tFragments N50:\t147964\n\tLargest frg:\t150253\n\tScaffolds:\t0\n\tMean coverage:\t16\n\n[2025-01-14 13:09:26] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/99/working/out_dir/assembly.fasta\n", "job_stdout": "", "job_stderr": "", "stderr": "[2025-01-14 13:09:15] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:09:15] INFO: >>>STAGE: configure\n[2025-01-14 13:09:15] INFO: Configuring run\n[2025-01-14 13:09:15] INFO: Total read length: 6522170\n[2025-01-14 13:09:15] INFO: Reads N50/N90: 2706 / 1386\n[2025-01-14 13:09:15] INFO: Selected minimum overlap: 1000\n[2025-01-14 13:09:15] INFO: >>>STAGE: assembly\n[2025-01-14 13:09:15] INFO: Assembling disjointigs\n[2025-01-14 13:09:15] INFO: Reading sequences\n[2025-01-14 13:09:15] INFO: Building minimizer index\n[2025-01-14 13:09:15] INFO: Pre-calculating index storage\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:16] INFO: Filling index\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:16] INFO: Extending reads\n[2025-01-14 13:09:19] INFO: Overlap-based coverage: 12\n[2025-01-14 13:09:19] INFO: Median overlap divergence: 0.0135674\n0% 10% 20% 30% 40% 70% 80% 90% 100% \n[2025-01-14 13:09:19] INFO: Assembled 11 disjointigs\n[2025-01-14 13:09:19] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:19] INFO: Filtering contained disjointigs\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:19] INFO: Contained seqs: 0\n[2025-01-14 13:09:19] INFO: >>>STAGE: consensus\n[2025-01-14 13:09:19] INFO: Running Minimap2\n[2025-01-14 13:09:20] INFO: Computing consensus\n[2025-01-14 13:09:21] INFO: Alignment error rate: 0.018082\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/99/tmp/pymp-n2s5mmme'\n[2025-01-14 13:09:21] INFO: >>>STAGE: repeat\n[2025-01-14 13:09:21] INFO: Building and resolving repeat graph\n[2025-01-14 13:09:21] INFO: Parsing disjointigs\n[2025-01-14 13:09:21] INFO: Building repeat graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:21] INFO: Median overlap divergence: 0.000980392\n[2025-01-14 13:09:21] INFO: Parsing reads\n[2025-01-14 13:09:21] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:09:22] INFO: Aligned read sequence: 6403986 / 6522170 (0.98188)\n[2025-01-14 13:09:22] INFO: Median overlap divergence: 0.00689656\n[2025-01-14 13:09:22] INFO: Mean edge coverage: 14\n[2025-01-14 13:09:22] INFO: Simplifying the graph\n[2025-01-14 13:09:22] INFO: >>>STAGE: contigger\n[2025-01-14 13:09:22] INFO: Generating contigs\n[2025-01-14 13:09:22] INFO: Reading sequences\n[2025-01-14 13:09:22] INFO: Generated 4 contigs\n[2025-01-14 13:09:22] INFO: Added 0 scaffold connections\n[2025-01-14 13:09:22] INFO: >>>STAGE: polishing\n[2025-01-14 13:09:22] INFO: Polishing genome (1/1)\n[2025-01-14 13:09:22] INFO: Running minimap2\n[2025-01-14 13:09:22] INFO: Separating alignment into bubbles\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/99/tmp/pymp-5kmiqtfe'\n[2025-01-14 13:09:24] INFO: Alignment error rate: 0.009628\n[2025-01-14 13:09:24] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/99/tmp/pymp-0620o1k5'\n[2025-01-14 13:09:26] INFO: >>>STAGE: finalize\n[2025-01-14 13:09:26] INFO: Assembly statistics:\n\n\tTotal length:\t419247\n\tFragments:\t4\n\tFragments N50:\t147964\n\tLargest frg:\t150253\n\tScaffolds:\t0\n\tMean coverage:\t16\n\n[2025-01-14 13:09:26] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/99/working/out_dir/assembly.fasta\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "11 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "11.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:09:26", "plugin": "core", "name": "end_epoch", "raw_value": "1736860166.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:09:15", "plugin": "core", "name": "start_epoch", "raw_value": "1736860155.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "flye/2.9.5+galaxy0-8", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.9.5+galaxy0", "test_index": 8, "time_seconds": 93.94497537612915, "inputs": {"inputs": {"src": "hda", "id": "21e493d2ea46479a"}, "mode_conditional|mode": "--nano-raw", "iterations": "0", "no_alt_contigs": true}, "job": {"model_class": "Job", "id": "632e5adf46c801b7", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:11:09.814085", "create_time": "2025-01-14T13:09:53.656888", "galaxy_version": "23.1", "command_version": "2.9.5-b1801", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-ht9dm", "command_line": "ln -sf '/galaxy/server/database/objects/1/f/3/dataset_1f3beea1-faa9-4eeb-815b-3066b5d118fb.dat' ./input_0.fasta.gz && flye --nano-raw ./input_0.fasta.gz -o out_dir -t ${GALAXY_SLOTS:-4} -i 0 --no-alt-contigs", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "generate_log": "false", "no_alt_contigs": "true", "asm": "{\"__current_case__\": 1, \"asm_select\": \"false\"}", "meta": "false", "scaffold": "false", "keep_haplotypes": "false", "min_overlap": "\"\"", "iterations": "\"0\"", "mode_conditional": "{\"__current_case__\": 0, \"mode\": \"--nano-raw\"}"}, "inputs": {"inputs": {"id": "21e493d2ea46479a", "src": "hda", "uuid": "1f3beea1-faa9-4eeb-815b-3066b5d118fb"}, "inputs1": {"id": "21e493d2ea46479a", "src": "hda", "uuid": "1f3beea1-faa9-4eeb-815b-3066b5d118fb"}}, "outputs": {"consensus": {"id": "62718f2315e178fd", "src": "hda", "uuid": "95142800-3815-4b27-8dac-74b0237754a6"}, "assembly_graph": {"id": "2107d80409536935", "src": "hda", "uuid": "8d224119-5996-482f-8802-a1565a8f2e5b"}, "assembly_gfa": {"id": "c699365c328d1506", "src": "hda", "uuid": "35bd5628-84e2-408a-9195-a89b2f796adc"}, "assembly_info": {"id": "5041413aebc05361", "src": "hda", "uuid": "0887dd4d-e494-4c85-a181-afc9bdac3466"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[2025-01-14 13:09:55] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:09:55] INFO: >>>STAGE: configure\n[2025-01-14 13:09:55] INFO: Configuring run\n[2025-01-14 13:09:55] INFO: Total read length: 1466260\n[2025-01-14 13:09:55] INFO: Reads N50/N90: 9054 / 4697\n[2025-01-14 13:09:55] INFO: Minimum overlap set to 5000\n[2025-01-14 13:09:55] INFO: >>>STAGE: assembly\n[2025-01-14 13:09:55] INFO: Assembling disjointigs\n[2025-01-14 13:09:55] INFO: Reading sequences\n[2025-01-14 13:10:00] INFO: Counting k-mers:\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:10:51] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:10:51] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:10:55] INFO: Extending reads\n[2025-01-14 13:10:58] INFO: Overlap-based coverage: 42\n[2025-01-14 13:10:58] INFO: Median overlap divergence: 0.105617\n0% 90% 100% \n[2025-01-14 13:10:58] INFO: Assembled 1 disjointigs\n[2025-01-14 13:10:58] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:10:58] INFO: Filtering contained disjointigs\n0% 100% \n[2025-01-14 13:10:58] INFO: Contained seqs: 0\n[2025-01-14 13:10:58] INFO: >>>STAGE: consensus\n[2025-01-14 13:10:58] INFO: Running Minimap2\n[2025-01-14 13:10:58] INFO: Computing consensus\n[2025-01-14 13:10:59] INFO: Alignment error rate: 0.175120\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/101/tmp/pymp-fr22sh1t'\n[2025-01-14 13:10:59] INFO: >>>STAGE: repeat\n[2025-01-14 13:10:59] INFO: Building and resolving repeat graph\n[2025-01-14 13:10:59] INFO: Parsing disjointigs\n[2025-01-14 13:10:59] INFO: Building repeat graph\n0% 100% \n[2025-01-14 13:11:00] INFO: Median overlap divergence: 0.0151003\n[2025-01-14 13:11:00] INFO: Parsing reads\n[2025-01-14 13:11:00] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:11:00] INFO: Aligned read sequence: 1166207 / 1313105 (0.888129)\n[2025-01-14 13:11:00] INFO: Median overlap divergence: 0.0550349\n[2025-01-14 13:11:00] INFO: Mean edge coverage: 33\n[2025-01-14 13:11:00] INFO: Simplifying the graph\n[2025-01-14 13:11:00] INFO: >>>STAGE: contigger\n[2025-01-14 13:11:00] INFO: Generating contigs\n[2025-01-14 13:11:00] INFO: Reading sequences\n[2025-01-14 13:11:00] INFO: Generated 1 contigs\n[2025-01-14 13:11:00] INFO: Added 0 scaffold connections\n[2025-01-14 13:11:00] INFO: >>>STAGE: finalize\n[2025-01-14 13:11:00] INFO: Assembly statistics:\n\n\tTotal length:\t5027\n\tFragments:\t1\n\tFragments N50:\t5027\n\tLargest frg:\t5027\n\tScaffolds:\t0\n\tMean coverage:\t95\n\n[2025-01-14 13:11:00] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/101/working/out_dir/assembly.fasta\n", "job_stdout": "", "job_stderr": "", "stderr": "[2025-01-14 13:09:55] INFO: Starting Flye 2.9.5-b1801\n[2025-01-14 13:09:55] INFO: >>>STAGE: configure\n[2025-01-14 13:09:55] INFO: Configuring run\n[2025-01-14 13:09:55] INFO: Total read length: 1466260\n[2025-01-14 13:09:55] INFO: Reads N50/N90: 9054 / 4697\n[2025-01-14 13:09:55] INFO: Minimum overlap set to 5000\n[2025-01-14 13:09:55] INFO: >>>STAGE: assembly\n[2025-01-14 13:09:55] INFO: Assembling disjointigs\n[2025-01-14 13:09:55] INFO: Reading sequences\n[2025-01-14 13:10:00] INFO: Counting k-mers:\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:10:51] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:10:51] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:10:55] INFO: Extending reads\n[2025-01-14 13:10:58] INFO: Overlap-based coverage: 42\n[2025-01-14 13:10:58] INFO: Median overlap divergence: 0.105617\n0% 90% 100% \n[2025-01-14 13:10:58] INFO: Assembled 1 disjointigs\n[2025-01-14 13:10:58] INFO: Generating sequence\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:10:58] INFO: Filtering contained disjointigs\n0% 100% \n[2025-01-14 13:10:58] INFO: Contained seqs: 0\n[2025-01-14 13:10:58] INFO: >>>STAGE: consensus\n[2025-01-14 13:10:58] INFO: Running Minimap2\n[2025-01-14 13:10:58] INFO: Computing consensus\n[2025-01-14 13:10:59] INFO: Alignment error rate: 0.175120\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 314, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.12/multiprocessing/process.py\", line 108, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 599, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.12/multiprocessing/managers.py\", line 184, 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/python3.12/multiprocessing/util.py\", line 303, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 227, in __call__\n res = self._callback(*self._args, **self._kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/multiprocessing/util.py\", line 136, in _remove_temp_dir\n rmtree(tempdir, onerror=onerror)\n File \"/usr/local/lib/python3.12/shutil.py\", line 759, in rmtree\n _rmtree_safe_fd(stack, onexc)\n File \"/usr/local/lib/python3.12/shutil.py\", line 703, in _rmtree_safe_fd\n onexc(func, path, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 700, in _rmtree_safe_fd\n onexc(os.unlink, fullname, err)\n File \"/usr/local/lib/python3.12/shutil.py\", line 750, in onexc\n return onerror(func, path, exc_info)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/shutil.py\", line 698, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/101/tmp/pymp-fr22sh1t'\n[2025-01-14 13:10:59] INFO: >>>STAGE: repeat\n[2025-01-14 13:10:59] INFO: Building and resolving repeat graph\n[2025-01-14 13:10:59] INFO: Parsing disjointigs\n[2025-01-14 13:10:59] INFO: Building repeat graph\n0% 100% \n[2025-01-14 13:11:00] INFO: Median overlap divergence: 0.0151003\n[2025-01-14 13:11:00] INFO: Parsing reads\n[2025-01-14 13:11:00] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2025-01-14 13:11:00] INFO: Aligned read sequence: 1166207 / 1313105 (0.888129)\n[2025-01-14 13:11:00] INFO: Median overlap divergence: 0.0550349\n[2025-01-14 13:11:00] INFO: Mean edge coverage: 33\n[2025-01-14 13:11:00] INFO: Simplifying the graph\n[2025-01-14 13:11:00] INFO: >>>STAGE: contigger\n[2025-01-14 13:11:00] INFO: Generating contigs\n[2025-01-14 13:11:00] INFO: Reading sequences\n[2025-01-14 13:11:00] INFO: Generated 1 contigs\n[2025-01-14 13:11:00] INFO: Added 0 scaffold connections\n[2025-01-14 13:11:00] INFO: >>>STAGE: finalize\n[2025-01-14 13:11:00] INFO: Assembly statistics:\n\n\tTotal length:\t5027\n\tFragments:\t1\n\tFragments N50:\t5027\n\tLargest frg:\t5027\n\tScaffolds:\t0\n\tMean coverage:\t95\n\n[2025-01-14 13:11:00] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/101/working/out_dir/assembly.fasta\n", "stdout": "", "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": "65.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:11:00", "plugin": "core", "name": "end_epoch", "raw_value": "1736860260.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:09:55", "plugin": "core", "name": "start_epoch", "raw_value": "1736860195.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-0", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 0, "time_seconds": 42.368667125701904, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "28a769a7a9fbe219"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "df311dc0f535cc73"}, "library|input_2": {"src": "hda", "id": "849c4e4d760318d4"}, "library|type": "paired", "adv|reporting_options|reporting_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "e86a040fdf95cf43", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:33:54.742105", "create_time": "2025-01-14T13:33:33.358247", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-q6tbz", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/9/2/0/dataset_920a8933-7b6e-495d-bf02-f8362665caf1.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/a/d/d/dataset_add2dfb5-228a-4708-91c5-58876f1cdf94.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/e/d/a/dataset_eda00435-56a7-4fe4-8aef-2583dd1dbe07.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/1/c/dataset_d1c88bc7-b96c-4b30-8031-236a940c4220.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\": 196, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 197, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 195, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "28a769a7a9fbe219", "src": "hda", "uuid": "920a8933-7b6e-495d-bf02-f8362665caf1"}, "library|input_1": {"id": "df311dc0f535cc73", "src": "hda", "uuid": "add2dfb5-228a-4708-91c5-58876f1cdf94"}, "library|input_2": {"id": "849c4e4d760318d4", "src": "hda", "uuid": "eda00435-56a7-4fe4-8aef-2583dd1dbe07"}}, "outputs": {"output_alignments": {"id": "03231a858175433d", "src": "hda", "uuid": "d1c88bc7-b96c-4b30-8031-236a940c4220"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Entering block accumulator loop for bucket 3:\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 3: 10%\n bucket 2: 10%\nGetting block 6 of 60\n Calculating Z arrays for bucket 5\n bucket 2: 20%\n bucket 1: 10%\n bucket 2: 30%\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 4\n bucket 3: 20%\n bucket 5: 10%\n bucket 2: 40%\n bucket 1: 20%\n Reserving size (126) for bucket 6\n bucket 5: 20%\nGetting block 7 of 60\nGetting block 8 of 60\n bucket 1: 30%\n Calculating Z arrays for bucket 6\n bucket 2: 50%\n bucket 5: 30%\n Calculating Z arrays for bucket 4\n bucket 2: 60%\n bucket 3: 30%\n Reserving size (126) for bucket 7\n Reserving size (126) for bucket 8\n bucket 1: 40%\n Calculating Z arrays for bucket 8\n bucket 3: 40%\n bucket 5: 40%\n Entering block accumulator loop for bucket 6:\n bucket 2: 70%\n Entering block accumulator loop for bucket 4:\n bucket 2: 80%\n bucket 1: 50%\n bucket 6: 10%\n Calculating Z arrays for bucket 7\n bucket 4: 10%\n bucket 6: 20%\n bucket 5: 50%\n bucket 3: 50%\n Entering block accumulator loop for bucket 8:\n bucket 2: 90%\n bucket 5: 60%\n bucket 1: 60%\n bucket 4: 20%\n bucket 3: 60%\n bucket 5: 70%\n bucket 6: 30%\n Entering block accumulator loop for bucket 7:\n bucket 8: 10%\n bucket 3: 70%\n bucket 2: 100%\n bucket 4: 30%\n bucket 3: 80%\n bucket 5: 80%\n bucket 6: 40%\n bucket 4: 40%\n bucket 5: 90%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 1: 70%\n bucket 7: 10%\n bucket 8: 20%\n bucket 5: 100%\n bucket 6: 50%\n bucket 4: 50%\n Sorting block of length 63 for bucket 5\n bucket 6: 60%\n bucket 7: 20%\n bucket 4: 60%\n bucket 6: 70%\n (Using difference cover)\n bucket 7: 30%\n bucket 8: 30%\n bucket 3: 90%\n bucket 1: 80%\n bucket 6: 80%\n bucket 8: 40%\n Sorting block time: 00:00:00\n bucket 7: 40%\n bucket 8: 50%\n bucket 7: 50%\n bucket 1: 90%\n bucket 7: 60%\n bucket 4: 70%\n bucket 6: 90%\nReturning block of 85 for bucket 2\n bucket 8: 60%\n bucket 3: 100%\n bucket 6: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 1: 100%\n bucket 8: 70%\n bucket 4: 80%\n Sorting block of length 42 for bucket 1\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 80%\n bucket 4: 90%\n bucket 7: 70%\n bucket 8: 90%\n (Using difference cover)\n bucket 7: 80%\n bucket 4: 100%\n bucket 8: 100%\n Sorting block of length 68 for bucket 4\n Sorting block of length 94 for bucket 8\n bucket 7: 90%\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\n Reserving size (126) for bucket 9\nGetting block 10 of 60\n Calculating Z arrays for bucket 9\n Reserving size (126) for bucket 10\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 9: 70%\n bucket 10: 70%\n bucket 9: 80%\n bucket 10: 80%\n bucket 9: 90%\n bucket 10: 90%\n bucket 10: 100%\n bucket 9: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Reserving size (126) for bucket 11\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 11: 10%\n bucket 12: 10%\n bucket 11: 20%\n bucket 12: 20%\n bucket 11: 30%\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 11: 90%\n bucket 12: 70%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\nGetting block 14 of 60\n bucket 13: 10%\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n Entering block accumulator loop for bucket 14:\n bucket 13: 50%\n bucket 14: 10%\n bucket 13: 60%\n bucket 14: 20%\n bucket 13: 70%\n bucket 14: 30%\n bucket 13: 80%\n bucket 14: 40%\n bucket 13: 90%\n bucket 14: 50%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n bucket 14: 60%\n (Using difference cover)\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n bucket 15: 20%\n Entering block accumulator loop for bucket 16:\n bucket 15: 30%\n bucket 16: 10%\n bucket 15: 40%\n bucket 16: 20%\n bucket 15: 50%\n bucket 16: 30%\n bucket 15: 60%\n bucket 16: 40%\n bucket 15: 70%\n bucket 16: 50%\n bucket 15: 80%\n bucket 16: 60%\n bucket 15: 90%\n bucket 16: 70%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Entering block accumulator loop for bucket 17:\n Reserving size (126) 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 18: 30%\n bucket 17: 60%\n bucket 18: 40%\n bucket 17: 70%\n bucket 18: 50%\n bucket 18: 60%\n bucket 17: 80%\n bucket 18: 70%\n bucket 17: 90%\n bucket 18: 80%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) 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 60\n bucket 19: 50%\n Reserving size (126) 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 19: 90%\n bucket 20: 10%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) 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 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) 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 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) 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 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) 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 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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%\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n bucket 26: 30%\n bucket 25: 30%\n Calculating Z arrays for bucket 27\n bucket 26: 40%\n bucket 25: 40%\n bucket 26: 50%\n bucket 25: 50%\n bucket 26: 60%\n bucket 25: 60%\n bucket 26: 70%\n Entering block accumulator loop for bucket 27:\n bucket 25: 70%\n bucket 26: 80%\n bucket 25: 80%\n bucket 27: 10%\n bucket 26: 90%\n bucket 25: 90%\n bucket 26: 100%\n bucket 25: 100%\n bucket 27: 20%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block of length 66 for bucket 25\n (Using difference cover)\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 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Reserving size (126) for bucket 28\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 28: 10%\n bucket 29: 20%\n bucket 28: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 28: 30%\n bucket 29: 50%\n bucket 28: 40%\n bucket 29: 60%\n bucket 28: 50%\n bucket 29: 70%\n bucket 28: 60%\n bucket 29: 80%\n bucket 28: 70%\n bucket 29: 90%\n bucket 28: 80%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 10%\n bucket 31: 30%\n bucket 33: 10%\n bucket 32: 20%\n bucket 31: 40%\n bucket 32: 30%\n bucket 31: 50%\n bucket 33: 20%\n bucket 32: 40%\n bucket 31: 60%\n bucket 33: 30%\n bucket 32: 50%\n bucket 31: 70%\n bucket 33: 40%\n bucket 32: 60%\n bucket 33: 50%\n bucket 31: 80%\n bucket 32: 70%\n bucket 31: 90%\n bucket 33: 60%\n bucket 32: 80%\n bucket 31: 100%\n bucket 33: 70%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n bucket 33: 80%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n bucket 34: 30%\n bucket 35: 10%\n bucket 34: 40%\n bucket 35: 20%\n bucket 34: 50%\n bucket 34: 60%\n bucket 35: 30%\n bucket 34: 70%\n bucket 35: 40%\n bucket 34: 80%\n bucket 34: 90%\n bucket 35: 50%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Entering block accumulator loop for bucket 36:\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n Entering block accumulator loop for bucket 37:\n bucket 36: 50%\n bucket 36: 60%\n bucket 37: 10%\n bucket 36: 70%\n bucket 36: 80%\n bucket 37: 20%\n bucket 36: 90%\n bucket 37: 30%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n bucket 39: 50%\n bucket 39: 60%\n Entering block accumulator loop for bucket 40:\n bucket 39: 70%\n bucket 40: 10%\n bucket 39: 80%\n bucket 40: 20%\n bucket 39: 90%\n bucket 40: 30%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 42: 10%\n bucket 41: 20%\n bucket 42: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 42: 30%\n bucket 41: 50%\n bucket 42: 40%\n bucket 41: 60%\n bucket 42: 50%\n bucket 41: 70%\n bucket 41: 80%\n bucket 42: 60%\n bucket 41: 90%\n bucket 42: 70%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Entering block accumulator loop for bucket 44:\n Calculating Z arrays for bucket 45\n bucket 44: 10%\n bucket 44: 20%\n Entering block accumulator loop for bucket 45:\n bucket 44: 30%\n bucket 45: 10%\n bucket 44: 40%\n bucket 44: 50%\n bucket 45: 20%\n bucket 44: 60%\n bucket 45: 30%\n bucket 44: 70%\n bucket 45: 40%\n bucket 44: 80%\n bucket 45: 50%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n bucket 46: 80%\n Calculating Z arrays for bucket 47\n bucket 46: 90%\n Entering block accumulator loop for bucket 47:\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 30%\n bucket 49: 40%\n Entering block accumulator loop for bucket 50:\n bucket 49: 50%\n bucket 50: 10%\n bucket 49: 60%\n bucket 50: 20%\n bucket 49: 70%\n bucket 50: 30%\n bucket 50: 40%\n bucket 49: 80%\n bucket 50: 50%\n bucket 49: 90%\n bucket 50: 60%\n bucket 50: 70%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\nGetting block 52 of 60\n Reserving size (126) for bucket 51\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 51\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 51:\n bucket 52: 10%\n bucket 51: 10%\n bucket 52: 20%\n bucket 51: 20%\n bucket 52: 30%\n bucket 52: 40%\n bucket 51: 30%\n bucket 52: 50%\n bucket 51: 40%\n bucket 52: 60%\n bucket 52: 70%\n bucket 51: 50%\n bucket 52: 80%\n bucket 51: 60%\n bucket 52: 90%\n bucket 52: 100%\n bucket 51: 70%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 54: 30%\n bucket 55: 20%\n bucket 54: 40%\n bucket 55: 30%\n bucket 55: 40%\n bucket 54: 50%\n bucket 55: 50%\n bucket 55: 60%\n bucket 54: 60%\n bucket 55: 70%\n bucket 54: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 54: 80%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\nGetting block 57 of 60\n bucket 56: 60%\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n Entering block accumulator loop for bucket 57:\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\nGetting block 60 of 60\n bucket 59: 10%\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 20%\n Entering block accumulator loop for bucket 60:\n bucket 59: 30%\n bucket 60: 10%\n bucket 59: 40%\n bucket 60: 20%\n bucket 60: 30%\n bucket 59: 50%\n bucket 60: 40%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 59: 80%\n bucket 60: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Entering block accumulator loop for bucket 3:\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 3: 10%\n bucket 2: 10%\nGetting block 6 of 60\n Calculating Z arrays for bucket 5\n bucket 2: 20%\n bucket 1: 10%\n bucket 2: 30%\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 4\n bucket 3: 20%\n bucket 5: 10%\n bucket 2: 40%\n bucket 1: 20%\n Reserving size (126) for bucket 6\n bucket 5: 20%\nGetting block 7 of 60\nGetting block 8 of 60\n bucket 1: 30%\n Calculating Z arrays for bucket 6\n bucket 2: 50%\n bucket 5: 30%\n Calculating Z arrays for bucket 4\n bucket 2: 60%\n bucket 3: 30%\n Reserving size (126) for bucket 7\n Reserving size (126) for bucket 8\n bucket 1: 40%\n Calculating Z arrays for bucket 8\n bucket 3: 40%\n bucket 5: 40%\n Entering block accumulator loop for bucket 6:\n bucket 2: 70%\n Entering block accumulator loop for bucket 4:\n bucket 2: 80%\n bucket 1: 50%\n bucket 6: 10%\n Calculating Z arrays for bucket 7\n bucket 4: 10%\n bucket 6: 20%\n bucket 5: 50%\n bucket 3: 50%\n Entering block accumulator loop for bucket 8:\n bucket 2: 90%\n bucket 5: 60%\n bucket 1: 60%\n bucket 4: 20%\n bucket 3: 60%\n bucket 5: 70%\n bucket 6: 30%\n Entering block accumulator loop for bucket 7:\n bucket 8: 10%\n bucket 3: 70%\n bucket 2: 100%\n bucket 4: 30%\n bucket 3: 80%\n bucket 5: 80%\n bucket 6: 40%\n bucket 4: 40%\n bucket 5: 90%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 1: 70%\n bucket 7: 10%\n bucket 8: 20%\n bucket 5: 100%\n bucket 6: 50%\n bucket 4: 50%\n Sorting block of length 63 for bucket 5\n bucket 6: 60%\n bucket 7: 20%\n bucket 4: 60%\n bucket 6: 70%\n (Using difference cover)\n bucket 7: 30%\n bucket 8: 30%\n bucket 3: 90%\n bucket 1: 80%\n bucket 6: 80%\n bucket 8: 40%\n Sorting block time: 00:00:00\n bucket 7: 40%\n bucket 8: 50%\n bucket 7: 50%\n bucket 1: 90%\n bucket 7: 60%\n bucket 4: 70%\n bucket 6: 90%\nReturning block of 85 for bucket 2\n bucket 8: 60%\n bucket 3: 100%\n bucket 6: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 1: 100%\n bucket 8: 70%\n bucket 4: 80%\n Sorting block of length 42 for bucket 1\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 80%\n bucket 4: 90%\n bucket 7: 70%\n bucket 8: 90%\n (Using difference cover)\n bucket 7: 80%\n bucket 4: 100%\n bucket 8: 100%\n Sorting block of length 68 for bucket 4\n Sorting block of length 94 for bucket 8\n bucket 7: 90%\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\n Reserving size (126) for bucket 9\nGetting block 10 of 60\n Calculating Z arrays for bucket 9\n Reserving size (126) for bucket 10\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 9: 70%\n bucket 10: 70%\n bucket 9: 80%\n bucket 10: 80%\n bucket 9: 90%\n bucket 10: 90%\n bucket 10: 100%\n bucket 9: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Reserving size (126) for bucket 11\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 11: 10%\n bucket 12: 10%\n bucket 11: 20%\n bucket 12: 20%\n bucket 11: 30%\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 11: 90%\n bucket 12: 70%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\nGetting block 14 of 60\n bucket 13: 10%\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n Entering block accumulator loop for bucket 14:\n bucket 13: 50%\n bucket 14: 10%\n bucket 13: 60%\n bucket 14: 20%\n bucket 13: 70%\n bucket 14: 30%\n bucket 13: 80%\n bucket 14: 40%\n bucket 13: 90%\n bucket 14: 50%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n bucket 14: 60%\n (Using difference cover)\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n bucket 15: 20%\n Entering block accumulator loop for bucket 16:\n bucket 15: 30%\n bucket 16: 10%\n bucket 15: 40%\n bucket 16: 20%\n bucket 15: 50%\n bucket 16: 30%\n bucket 15: 60%\n bucket 16: 40%\n bucket 15: 70%\n bucket 16: 50%\n bucket 15: 80%\n bucket 16: 60%\n bucket 15: 90%\n bucket 16: 70%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Entering block accumulator loop for bucket 17:\n Reserving size (126) 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 18: 30%\n bucket 17: 60%\n bucket 18: 40%\n bucket 17: 70%\n bucket 18: 50%\n bucket 18: 60%\n bucket 17: 80%\n bucket 18: 70%\n bucket 17: 90%\n bucket 18: 80%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) 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 60\n bucket 19: 50%\n Reserving size (126) 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 19: 90%\n bucket 20: 10%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) 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 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) 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 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) 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 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) 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 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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%\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n bucket 26: 30%\n bucket 25: 30%\n Calculating Z arrays for bucket 27\n bucket 26: 40%\n bucket 25: 40%\n bucket 26: 50%\n bucket 25: 50%\n bucket 26: 60%\n bucket 25: 60%\n bucket 26: 70%\n Entering block accumulator loop for bucket 27:\n bucket 25: 70%\n bucket 26: 80%\n bucket 25: 80%\n bucket 27: 10%\n bucket 26: 90%\n bucket 25: 90%\n bucket 26: 100%\n bucket 25: 100%\n bucket 27: 20%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block of length 66 for bucket 25\n (Using difference cover)\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 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Reserving size (126) for bucket 28\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 28: 10%\n bucket 29: 20%\n bucket 28: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 28: 30%\n bucket 29: 50%\n bucket 28: 40%\n bucket 29: 60%\n bucket 28: 50%\n bucket 29: 70%\n bucket 28: 60%\n bucket 29: 80%\n bucket 28: 70%\n bucket 29: 90%\n bucket 28: 80%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 10%\n bucket 31: 30%\n bucket 33: 10%\n bucket 32: 20%\n bucket 31: 40%\n bucket 32: 30%\n bucket 31: 50%\n bucket 33: 20%\n bucket 32: 40%\n bucket 31: 60%\n bucket 33: 30%\n bucket 32: 50%\n bucket 31: 70%\n bucket 33: 40%\n bucket 32: 60%\n bucket 33: 50%\n bucket 31: 80%\n bucket 32: 70%\n bucket 31: 90%\n bucket 33: 60%\n bucket 32: 80%\n bucket 31: 100%\n bucket 33: 70%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n bucket 33: 80%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n bucket 34: 30%\n bucket 35: 10%\n bucket 34: 40%\n bucket 35: 20%\n bucket 34: 50%\n bucket 34: 60%\n bucket 35: 30%\n bucket 34: 70%\n bucket 35: 40%\n bucket 34: 80%\n bucket 34: 90%\n bucket 35: 50%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Entering block accumulator loop for bucket 36:\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n Entering block accumulator loop for bucket 37:\n bucket 36: 50%\n bucket 36: 60%\n bucket 37: 10%\n bucket 36: 70%\n bucket 36: 80%\n bucket 37: 20%\n bucket 36: 90%\n bucket 37: 30%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n bucket 39: 50%\n bucket 39: 60%\n Entering block accumulator loop for bucket 40:\n bucket 39: 70%\n bucket 40: 10%\n bucket 39: 80%\n bucket 40: 20%\n bucket 39: 90%\n bucket 40: 30%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 42: 10%\n bucket 41: 20%\n bucket 42: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 42: 30%\n bucket 41: 50%\n bucket 42: 40%\n bucket 41: 60%\n bucket 42: 50%\n bucket 41: 70%\n bucket 41: 80%\n bucket 42: 60%\n bucket 41: 90%\n bucket 42: 70%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Entering block accumulator loop for bucket 44:\n Calculating Z arrays for bucket 45\n bucket 44: 10%\n bucket 44: 20%\n Entering block accumulator loop for bucket 45:\n bucket 44: 30%\n bucket 45: 10%\n bucket 44: 40%\n bucket 44: 50%\n bucket 45: 20%\n bucket 44: 60%\n bucket 45: 30%\n bucket 44: 70%\n bucket 45: 40%\n bucket 44: 80%\n bucket 45: 50%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n bucket 46: 80%\n Calculating Z arrays for bucket 47\n bucket 46: 90%\n Entering block accumulator loop for bucket 47:\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 30%\n bucket 49: 40%\n Entering block accumulator loop for bucket 50:\n bucket 49: 50%\n bucket 50: 10%\n bucket 49: 60%\n bucket 50: 20%\n bucket 49: 70%\n bucket 50: 30%\n bucket 50: 40%\n bucket 49: 80%\n bucket 50: 50%\n bucket 49: 90%\n bucket 50: 60%\n bucket 50: 70%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\nGetting block 52 of 60\n Reserving size (126) for bucket 51\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 51\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 51:\n bucket 52: 10%\n bucket 51: 10%\n bucket 52: 20%\n bucket 51: 20%\n bucket 52: 30%\n bucket 52: 40%\n bucket 51: 30%\n bucket 52: 50%\n bucket 51: 40%\n bucket 52: 60%\n bucket 52: 70%\n bucket 51: 50%\n bucket 52: 80%\n bucket 51: 60%\n bucket 52: 90%\n bucket 52: 100%\n bucket 51: 70%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 54: 30%\n bucket 55: 20%\n bucket 54: 40%\n bucket 55: 30%\n bucket 55: 40%\n bucket 54: 50%\n bucket 55: 50%\n bucket 55: 60%\n bucket 54: 60%\n bucket 55: 70%\n bucket 54: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 54: 80%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\nGetting block 57 of 60\n bucket 56: 60%\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n Entering block accumulator loop for bucket 57:\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\nGetting block 60 of 60\n bucket 59: 10%\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 20%\n Entering block accumulator loop for bucket 60:\n bucket 59: 30%\n bucket 60: 10%\n bucket 59: 40%\n bucket 60: 20%\n bucket 60: 30%\n bucket 59: 50%\n bucket 60: 40%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 59: 80%\n bucket 60: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:33:43", "plugin": "core", "name": "end_epoch", "raw_value": "1736861623.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:33:42", "plugin": "core", "name": "start_epoch", "raw_value": "1736861622.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 33.92935490608215, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "8726166f632f1381"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "b05013cc3624a825"}, "library|input_2": {"src": "hda", "id": "ab8c61ce197d5a3d"}, "library|type": "paired"}, "job": {"model_class": "Job", "id": "cff54bd4b52f88a2", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:34:28.702454", "create_time": "2025-01-14T13:34:15.701589", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-c2l56", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/1/e/1/dataset_1e17bace-bd92-4160-9a85-d01d812a914a.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/4/e/d/dataset_4ed5fc24-2b77-4d06-b8fb-089e915e928d.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/8/4/d/dataset_84dc0e98-b0a4-4623-aa23-7026aca9b7a1.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/b/3/1/dataset_b315e78f-5caf-4072-bfc8-386806b7ab6b.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\": 200, \"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\": 199, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "8726166f632f1381", "src": "hda", "uuid": "1e17bace-bd92-4160-9a85-d01d812a914a"}, "library|input_1": {"id": "b05013cc3624a825", "src": "hda", "uuid": "4ed5fc24-2b77-4d06-b8fb-089e915e928d"}, "library|input_2": {"id": "ab8c61ce197d5a3d", "src": "hda", "uuid": "84dc0e98-b0a4-4623-aa23-7026aca9b7a1"}}, "outputs": {"output_alignments": {"id": "8135e9623b001a0b", "src": "hda", "uuid": "b315e78f-5caf-4072-bfc8-386806b7ab6b"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\nGetting block 4 of 60\n Calculating Z arrays for bucket 3\n bucket 2: 10%\n bucket 1: 10%\nGetting block 6 of 60\n bucket 2: 20%\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n Calculating Z arrays for bucket 4\n bucket 1: 20%\n Reserving size (126) for bucket 5\nGetting block 7 of 60\n Entering block accumulator loop for bucket 3:\n bucket 1: 30%\n Calculating Z arrays for bucket 5\n Reserving size (126) for bucket 6\n bucket 3: 10%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 7\n bucket 3: 20%\n bucket 4: 10%\n bucket 2: 30%\n bucket 1: 40%\n Entering block accumulator loop for bucket 6:\n bucket 4: 20%\n Entering block accumulator loop for bucket 5:\n bucket 3: 30%\n bucket 1: 50%\n bucket 4: 30%\nGetting block 8 of 60\n bucket 2: 40%\n bucket 1: 60%\n Entering block accumulator loop for bucket 7:\n bucket 2: 50%\n bucket 4: 40%\n Reserving size (126) for bucket 8\n bucket 1: 70%\n bucket 6: 10%\n Calculating Z arrays for bucket 8\n bucket 4: 50%\n bucket 2: 60%\n bucket 5: 10%\n bucket 4: 60%\n bucket 6: 20%\n Entering block accumulator loop for bucket 8:\n bucket 2: 70%\n bucket 1: 80%\n bucket 3: 40%\n bucket 6: 30%\n bucket 2: 80%\n bucket 4: 70%\n bucket 5: 20%\n bucket 8: 10%\n bucket 3: 50%\n bucket 4: 80%\n bucket 2: 90%\n bucket 1: 90%\n bucket 6: 40%\n bucket 4: 90%\n bucket 2: 100%\n bucket 8: 20%\n bucket 1: 100%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 5: 30%\n bucket 3: 60%\n bucket 4: 100%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 7: 10%\n bucket 8: 30%\n bucket 3: 70%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 5: 40%\n bucket 6: 50%\n bucket 3: 80%\n bucket 8: 40%\n bucket 6: 60%\n bucket 5: 50%\n bucket 3: 90%\n bucket 6: 70%\n bucket 7: 20%\n bucket 8: 50%\n bucket 3: 100%\n bucket 6: 80%\n bucket 5: 60%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 60%\n bucket 7: 30%\n bucket 6: 90%\n bucket 5: 70%\n bucket 8: 70%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 5: 80%\n bucket 8: 80%\n bucket 7: 40%\n bucket 5: 90%\n bucket 8: 90%\n bucket 7: 50%\n bucket 5: 100%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 7: 60%\n Sorting block of length 63 for bucket 5\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 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\nGetting block 9 of 60\n Reserving size (126) 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 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\n Entering block accumulator loop for bucket 10:\nReturning block of 125 for bucket 9\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 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) 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%\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\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 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) 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 60\n bucket 13: 40%\n Reserving size (126) for bucket 14\n bucket 13: 50%\n Calculating Z arrays for bucket 14\n bucket 13: 60%\n bucket 13: 70%\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 85 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 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Entering block accumulator loop for bucket 15:\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n bucket 15: 20%\n Entering block accumulator loop for bucket 16:\n bucket 15: 30%\n bucket 16: 10%\n bucket 15: 40%\n bucket 16: 20%\n bucket 15: 50%\n bucket 16: 30%\n bucket 15: 60%\n bucket 16: 40%\n bucket 15: 70%\n bucket 16: 50%\n bucket 15: 80%\n bucket 16: 60%\n bucket 15: 90%\n bucket 16: 70%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n Entering block accumulator loop for bucket 18:\n bucket 17: 20%\n bucket 17: 30%\n bucket 18: 10%\n bucket 17: 40%\n bucket 18: 20%\n bucket 17: 50%\n bucket 18: 30%\n bucket 17: 60%\n bucket 18: 40%\n bucket 17: 70%\n bucket 18: 50%\n bucket 17: 80%\n bucket 18: 60%\n bucket 17: 90%\n bucket 18: 70%\n bucket 17: 100%\n bucket 18: 80%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 19 of 60\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Reserving size (126) for bucket 19\n Calculating Z arrays 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 Entering block accumulator loop for bucket 19:\n bucket 20: 60%\n bucket 20: 70%\n bucket 19: 10%\n bucket 20: 80%\n bucket 19: 20%\n bucket 20: 90%\n bucket 19: 30%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\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 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Entering block accumulator loop for bucket 21:\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 10%\n bucket 21: 20%\n Entering block accumulator loop for bucket 22:\n bucket 21: 30%\n bucket 22: 10%\n bucket 21: 40%\n bucket 22: 20%\n bucket 21: 50%\n bucket 22: 30%\n bucket 21: 60%\n bucket 22: 40%\n bucket 21: 70%\n bucket 22: 50%\n bucket 21: 80%\n bucket 22: 60%\n bucket 21: 90%\n bucket 22: 70%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 24: 10%\n bucket 23: 30%\n bucket 24: 20%\n bucket 23: 40%\n bucket 24: 30%\n bucket 23: 50%\n bucket 24: 40%\n bucket 23: 60%\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n bucket 24: 90%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) 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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 60\n Entering block accumulator loop for bucket 27:\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 10%\n bucket 27: 20%\n Entering block accumulator loop for bucket 28:\n bucket 27: 30%\n bucket 28: 10%\n bucket 27: 40%\n bucket 28: 20%\n bucket 27: 50%\n bucket 28: 30%\n bucket 27: 60%\n bucket 28: 40%\n bucket 27: 70%\n bucket 28: 50%\n bucket 27: 80%\n bucket 28: 60%\n bucket 27: 90%\n bucket 28: 70%\n bucket 28: 80%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n bucket 28: 90%\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) 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 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\nGetting block 31 of 60\n bucket 30: 20%\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 30: 30%\n bucket 30: 40%\n Entering block accumulator loop for bucket 31:\n bucket 30: 50%\n bucket 30: 60%\n bucket 31: 10%\n bucket 30: 70%\n bucket 31: 20%\n bucket 30: 80%\n bucket 31: 30%\n bucket 30: 90%\n bucket 31: 40%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n bucket 31: 50%\n (Using difference cover)\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Entering block accumulator loop for bucket 32:\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 10%\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 30%\n bucket 32: 40%\n bucket 33: 10%\n bucket 32: 50%\n bucket 33: 20%\n bucket 32: 60%\n bucket 33: 30%\n bucket 32: 70%\n bucket 33: 40%\n bucket 32: 80%\n bucket 33: 50%\n bucket 32: 90%\n bucket 33: 60%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Entering block accumulator loop for bucket 36:\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n Entering block accumulator loop for bucket 37:\n bucket 36: 20%\n bucket 37: 10%\n bucket 36: 30%\n bucket 37: 20%\n bucket 36: 40%\n bucket 37: 30%\n bucket 36: 50%\n bucket 37: 40%\n bucket 37: 50%\n bucket 36: 60%\n bucket 37: 60%\n bucket 36: 70%\n bucket 37: 70%\n bucket 37: 80%\n bucket 36: 80%\n bucket 37: 90%\n bucket 36: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\nGetting block 39 of 60\n bucket 38: 30%\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n Entering block accumulator loop for bucket 39:\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n bucket 39: 10%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Entering block accumulator loop for bucket 40:\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 10%\n Entering block accumulator loop for bucket 41:\n bucket 40: 20%\n bucket 41: 10%\n bucket 40: 30%\n bucket 41: 20%\n bucket 40: 40%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 40: 60%\n bucket 41: 50%\n bucket 40: 70%\n bucket 41: 60%\n bucket 40: 80%\n bucket 41: 70%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 40%\n bucket 42: 50%\n Entering block accumulator loop for bucket 43:\n bucket 42: 60%\n bucket 43: 10%\n bucket 42: 70%\n bucket 43: 20%\n bucket 43: 30%\n bucket 42: 80%\n bucket 43: 40%\n bucket 43: 50%\n bucket 42: 90%\n bucket 43: 60%\n bucket 43: 70%\n bucket 42: 100%\n bucket 43: 80%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n Entering block accumulator loop for bucket 46:\n bucket 45: 50%\n bucket 45: 60%\n bucket 46: 10%\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 20%\n bucket 45: 90%\n bucket 46: 30%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Entering block accumulator loop for bucket 47:\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n Entering block accumulator loop for bucket 48:\n bucket 47: 20%\n bucket 47: 30%\n bucket 48: 10%\n bucket 47: 40%\n bucket 48: 20%\n bucket 47: 50%\n bucket 48: 30%\n bucket 47: 60%\n bucket 48: 40%\n bucket 47: 70%\n bucket 48: 50%\n bucket 47: 80%\n bucket 47: 90%\n bucket 48: 60%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Reserving size (126) for bucket 52\n bucket 51: 10%\n Calculating Z arrays for bucket 53\n Calculating Z arrays for bucket 52\n bucket 51: 20%\n Entering block accumulator loop for bucket 53:\n bucket 51: 30%\n Entering block accumulator loop for bucket 52:\n bucket 51: 40%\n bucket 53: 10%\n bucket 51: 50%\n bucket 52: 10%\n bucket 53: 20%\n bucket 51: 60%\n bucket 53: 30%\n bucket 52: 20%\n bucket 51: 70%\n bucket 53: 40%\n bucket 51: 80%\n bucket 53: 50%\n bucket 52: 30%\n bucket 51: 90%\n bucket 53: 60%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n bucket 53: 70%\n (Using difference cover)\n bucket 52: 40%\n bucket 53: 80%\n bucket 53: 90%\n bucket 52: 50%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 60%\n bucket 55: 70%\n Entering block accumulator loop for bucket 56:\n bucket 55: 80%\n bucket 55: 90%\n bucket 56: 10%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n Sorting block time: 00:00:00\n bucket 56: 100%\nReturning block of 80 for bucket 55\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 58:\n bucket 59: 10%\n bucket 58: 10%\n bucket 59: 20%\n bucket 58: 20%\n bucket 59: 30%\n bucket 58: 30%\n bucket 59: 40%\n bucket 58: 40%\n bucket 59: 50%\n bucket 58: 50%\n bucket 59: 60%\n bucket 58: 60%\n bucket 59: 70%\n bucket 58: 70%\n bucket 59: 80%\n bucket 58: 80%\n bucket 59: 90%\n bucket 58: 90%\n bucket 59: 100%\n bucket 58: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\nGetting block 4 of 60\n Calculating Z arrays for bucket 3\n bucket 2: 10%\n bucket 1: 10%\nGetting block 6 of 60\n bucket 2: 20%\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n Calculating Z arrays for bucket 4\n bucket 1: 20%\n Reserving size (126) for bucket 5\nGetting block 7 of 60\n Entering block accumulator loop for bucket 3:\n bucket 1: 30%\n Calculating Z arrays for bucket 5\n Reserving size (126) for bucket 6\n bucket 3: 10%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 7\n bucket 3: 20%\n bucket 4: 10%\n bucket 2: 30%\n bucket 1: 40%\n Entering block accumulator loop for bucket 6:\n bucket 4: 20%\n Entering block accumulator loop for bucket 5:\n bucket 3: 30%\n bucket 1: 50%\n bucket 4: 30%\nGetting block 8 of 60\n bucket 2: 40%\n bucket 1: 60%\n Entering block accumulator loop for bucket 7:\n bucket 2: 50%\n bucket 4: 40%\n Reserving size (126) for bucket 8\n bucket 1: 70%\n bucket 6: 10%\n Calculating Z arrays for bucket 8\n bucket 4: 50%\n bucket 2: 60%\n bucket 5: 10%\n bucket 4: 60%\n bucket 6: 20%\n Entering block accumulator loop for bucket 8:\n bucket 2: 70%\n bucket 1: 80%\n bucket 3: 40%\n bucket 6: 30%\n bucket 2: 80%\n bucket 4: 70%\n bucket 5: 20%\n bucket 8: 10%\n bucket 3: 50%\n bucket 4: 80%\n bucket 2: 90%\n bucket 1: 90%\n bucket 6: 40%\n bucket 4: 90%\n bucket 2: 100%\n bucket 8: 20%\n bucket 1: 100%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 5: 30%\n bucket 3: 60%\n bucket 4: 100%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 7: 10%\n bucket 8: 30%\n bucket 3: 70%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 5: 40%\n bucket 6: 50%\n bucket 3: 80%\n bucket 8: 40%\n bucket 6: 60%\n bucket 5: 50%\n bucket 3: 90%\n bucket 6: 70%\n bucket 7: 20%\n bucket 8: 50%\n bucket 3: 100%\n bucket 6: 80%\n bucket 5: 60%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 60%\n bucket 7: 30%\n bucket 6: 90%\n bucket 5: 70%\n bucket 8: 70%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 5: 80%\n bucket 8: 80%\n bucket 7: 40%\n bucket 5: 90%\n bucket 8: 90%\n bucket 7: 50%\n bucket 5: 100%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 7: 60%\n Sorting block of length 63 for bucket 5\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 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\nGetting block 9 of 60\n Reserving size (126) 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 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\n Entering block accumulator loop for bucket 10:\nReturning block of 125 for bucket 9\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 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) 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%\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\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 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) 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 60\n bucket 13: 40%\n Reserving size (126) for bucket 14\n bucket 13: 50%\n Calculating Z arrays for bucket 14\n bucket 13: 60%\n bucket 13: 70%\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 85 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 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Entering block accumulator loop for bucket 15:\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n bucket 15: 20%\n Entering block accumulator loop for bucket 16:\n bucket 15: 30%\n bucket 16: 10%\n bucket 15: 40%\n bucket 16: 20%\n bucket 15: 50%\n bucket 16: 30%\n bucket 15: 60%\n bucket 16: 40%\n bucket 15: 70%\n bucket 16: 50%\n bucket 15: 80%\n bucket 16: 60%\n bucket 15: 90%\n bucket 16: 70%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n Entering block accumulator loop for bucket 18:\n bucket 17: 20%\n bucket 17: 30%\n bucket 18: 10%\n bucket 17: 40%\n bucket 18: 20%\n bucket 17: 50%\n bucket 18: 30%\n bucket 17: 60%\n bucket 18: 40%\n bucket 17: 70%\n bucket 18: 50%\n bucket 17: 80%\n bucket 18: 60%\n bucket 17: 90%\n bucket 18: 70%\n bucket 17: 100%\n bucket 18: 80%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 19 of 60\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Reserving size (126) for bucket 19\n Calculating Z arrays 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 Entering block accumulator loop for bucket 19:\n bucket 20: 60%\n bucket 20: 70%\n bucket 19: 10%\n bucket 20: 80%\n bucket 19: 20%\n bucket 20: 90%\n bucket 19: 30%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\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 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Entering block accumulator loop for bucket 21:\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 10%\n bucket 21: 20%\n Entering block accumulator loop for bucket 22:\n bucket 21: 30%\n bucket 22: 10%\n bucket 21: 40%\n bucket 22: 20%\n bucket 21: 50%\n bucket 22: 30%\n bucket 21: 60%\n bucket 22: 40%\n bucket 21: 70%\n bucket 22: 50%\n bucket 21: 80%\n bucket 22: 60%\n bucket 21: 90%\n bucket 22: 70%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 24: 10%\n bucket 23: 30%\n bucket 24: 20%\n bucket 23: 40%\n bucket 24: 30%\n bucket 23: 50%\n bucket 24: 40%\n bucket 23: 60%\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n bucket 24: 90%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) 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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 60\n Entering block accumulator loop for bucket 27:\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 10%\n bucket 27: 20%\n Entering block accumulator loop for bucket 28:\n bucket 27: 30%\n bucket 28: 10%\n bucket 27: 40%\n bucket 28: 20%\n bucket 27: 50%\n bucket 28: 30%\n bucket 27: 60%\n bucket 28: 40%\n bucket 27: 70%\n bucket 28: 50%\n bucket 27: 80%\n bucket 28: 60%\n bucket 27: 90%\n bucket 28: 70%\n bucket 28: 80%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n bucket 28: 90%\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) 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 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\nGetting block 31 of 60\n bucket 30: 20%\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 30: 30%\n bucket 30: 40%\n Entering block accumulator loop for bucket 31:\n bucket 30: 50%\n bucket 30: 60%\n bucket 31: 10%\n bucket 30: 70%\n bucket 31: 20%\n bucket 30: 80%\n bucket 31: 30%\n bucket 30: 90%\n bucket 31: 40%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n bucket 31: 50%\n (Using difference cover)\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Entering block accumulator loop for bucket 32:\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 10%\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 30%\n bucket 32: 40%\n bucket 33: 10%\n bucket 32: 50%\n bucket 33: 20%\n bucket 32: 60%\n bucket 33: 30%\n bucket 32: 70%\n bucket 33: 40%\n bucket 32: 80%\n bucket 33: 50%\n bucket 32: 90%\n bucket 33: 60%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Entering block accumulator loop for bucket 36:\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n Entering block accumulator loop for bucket 37:\n bucket 36: 20%\n bucket 37: 10%\n bucket 36: 30%\n bucket 37: 20%\n bucket 36: 40%\n bucket 37: 30%\n bucket 36: 50%\n bucket 37: 40%\n bucket 37: 50%\n bucket 36: 60%\n bucket 37: 60%\n bucket 36: 70%\n bucket 37: 70%\n bucket 37: 80%\n bucket 36: 80%\n bucket 37: 90%\n bucket 36: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\nGetting block 39 of 60\n bucket 38: 30%\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n Entering block accumulator loop for bucket 39:\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n bucket 39: 10%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Entering block accumulator loop for bucket 40:\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 10%\n Entering block accumulator loop for bucket 41:\n bucket 40: 20%\n bucket 41: 10%\n bucket 40: 30%\n bucket 41: 20%\n bucket 40: 40%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 40: 60%\n bucket 41: 50%\n bucket 40: 70%\n bucket 41: 60%\n bucket 40: 80%\n bucket 41: 70%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 40%\n bucket 42: 50%\n Entering block accumulator loop for bucket 43:\n bucket 42: 60%\n bucket 43: 10%\n bucket 42: 70%\n bucket 43: 20%\n bucket 43: 30%\n bucket 42: 80%\n bucket 43: 40%\n bucket 43: 50%\n bucket 42: 90%\n bucket 43: 60%\n bucket 43: 70%\n bucket 42: 100%\n bucket 43: 80%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n Entering block accumulator loop for bucket 46:\n bucket 45: 50%\n bucket 45: 60%\n bucket 46: 10%\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 20%\n bucket 45: 90%\n bucket 46: 30%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Entering block accumulator loop for bucket 47:\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n Entering block accumulator loop for bucket 48:\n bucket 47: 20%\n bucket 47: 30%\n bucket 48: 10%\n bucket 47: 40%\n bucket 48: 20%\n bucket 47: 50%\n bucket 48: 30%\n bucket 47: 60%\n bucket 48: 40%\n bucket 47: 70%\n bucket 48: 50%\n bucket 47: 80%\n bucket 47: 90%\n bucket 48: 60%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Reserving size (126) for bucket 52\n bucket 51: 10%\n Calculating Z arrays for bucket 53\n Calculating Z arrays for bucket 52\n bucket 51: 20%\n Entering block accumulator loop for bucket 53:\n bucket 51: 30%\n Entering block accumulator loop for bucket 52:\n bucket 51: 40%\n bucket 53: 10%\n bucket 51: 50%\n bucket 52: 10%\n bucket 53: 20%\n bucket 51: 60%\n bucket 53: 30%\n bucket 52: 20%\n bucket 51: 70%\n bucket 53: 40%\n bucket 51: 80%\n bucket 53: 50%\n bucket 52: 30%\n bucket 51: 90%\n bucket 53: 60%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n bucket 53: 70%\n (Using difference cover)\n bucket 52: 40%\n bucket 53: 80%\n bucket 53: 90%\n bucket 52: 50%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 60%\n bucket 55: 70%\n Entering block accumulator loop for bucket 56:\n bucket 55: 80%\n bucket 55: 90%\n bucket 56: 10%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n Sorting block time: 00:00:00\n bucket 56: 100%\nReturning block of 80 for bucket 55\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 58:\n bucket 59: 10%\n bucket 58: 10%\n bucket 59: 20%\n bucket 58: 20%\n bucket 59: 30%\n bucket 58: 30%\n bucket 59: 40%\n bucket 58: 40%\n bucket 59: 50%\n bucket 58: 50%\n bucket 59: 60%\n bucket 58: 60%\n bucket 59: 70%\n bucket 58: 70%\n bucket 59: 80%\n bucket 58: 80%\n bucket 59: 90%\n bucket 58: 90%\n bucket 59: 100%\n bucket 58: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:34:18", "plugin": "core", "name": "end_epoch", "raw_value": "1736861658.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:34:18", "plugin": "core", "name": "start_epoch", "raw_value": "1736861658.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 29.62270474433899, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "918b49d6c5b6b8d5"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "a7ed900389215d13"}, "library|rna_strandness": "R", "library|type": "single", "sum|new_summary": true, "sum|summary_file": true}, "job": {"model_class": "Job", "id": "68772c242e331cd3", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:39:38.946533", "create_time": "2025-01-14T13:39:27.065634", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-fmdjp", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/5/1/6/dataset_5161190a-a1e2-4915-8b95-e0848c79e578.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/b/b/4/dataset_bb4a53a5-4308-44c7-90d2-ce623f153830.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/f/3/7/dataset_f3717855-cf3a-4a41-b990-cc92a47b05cf.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\": 237, \"src\": \"hda\"}]}, \"rna_strandness\": \"R\", \"type\": \"single\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 236, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "918b49d6c5b6b8d5", "src": "hda", "uuid": "5161190a-a1e2-4915-8b95-e0848c79e578"}, "library|input_1": {"id": "a7ed900389215d13", "src": "hda", "uuid": "bb4a53a5-4308-44c7-90d2-ce623f153830"}}, "outputs": {"output_alignments": {"id": "00937496816bb428", "src": "hda", "uuid": "f3717855-cf3a-4a41-b990-cc92a47b05cf"}, "summary_file": {"id": "22ae62e0e0fb91ad", "src": "hda", "uuid": "9ae55147-b6ec-43a8-a3af-0918b63c4fe4"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 2 of 60\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Reserving size (126) for bucket 2\nGetting block 3 of 60\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\nGetting block 4 of 60\nGetting block 5 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 4\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 4\n Reserving size (126) for bucket 5\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 5\nGetting block 7 of 60\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 7\n bucket 4: 10%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 5:\nGetting block 8 of 60\n bucket 4: 20%\n bucket 5: 10%\n Calculating Z arrays for bucket 7\n bucket 1: 20%\n bucket 2: 10%\n bucket 5: 20%\n bucket 1: 30%\n Entering block accumulator loop for bucket 3:\n Reserving size (126) for bucket 8\n bucket 5: 30%\n Entering block accumulator loop for bucket 7:\n bucket 2: 20%\n bucket 5: 40%\n bucket 4: 30%\n bucket 7: 10%\n Calculating Z arrays for bucket 8\n bucket 2: 30%\n bucket 5: 50%\n bucket 1: 40%\n bucket 4: 40%\n bucket 3: 10%\n bucket 4: 50%\n bucket 5: 60%\n bucket 7: 20%\n Entering block accumulator loop for bucket 8:\n bucket 2: 40%\n bucket 3: 20%\n bucket 1: 50%\n bucket 7: 30%\n bucket 4: 60%\n bucket 6: 10%\n bucket 2: 50%\n bucket 4: 70%\n bucket 1: 60%\n bucket 7: 40%\n bucket 8: 10%\n bucket 3: 30%\n bucket 7: 50%\n bucket 2: 60%\n bucket 8: 20%\n bucket 6: 20%\n bucket 1: 70%\n bucket 4: 80%\n bucket 7: 60%\n bucket 2: 70%\n bucket 5: 70%\n bucket 1: 80%\n bucket 4: 90%\n bucket 8: 30%\n bucket 5: 80%\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 1: 90%\n bucket 7: 70%\n bucket 6: 30%\n bucket 1: 100%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 7: 80%\n bucket 8: 40%\n bucket 5: 90%\n bucket 7: 90%\n bucket 2: 80%\n bucket 6: 40%\n bucket 5: 100%\n bucket 7: 100%\n bucket 2: 90%\n bucket 3: 40%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 50%\n bucket 2: 100%\n bucket 3: 50%\n bucket 6: 50%\n bucket 8: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 6: 60%\n bucket 3: 60%\n Sorting block of length 75 for bucket 7\n bucket 6: 70%\n (Using difference cover)\n bucket 8: 70%\n bucket 6: 80%\n bucket 3: 70%\n bucket 8: 80%\n bucket 6: 90%\n bucket 3: 80%\n bucket 8: 90%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 3: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 3: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) 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%\nGetting block 10 of 60\n bucket 9: 80%\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 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 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n Entering block accumulator loop for bucket 11:\n bucket 12: 30%\n bucket 11: 10%\n bucket 12: 40%\n bucket 11: 20%\n bucket 12: 50%\n bucket 11: 30%\n bucket 12: 60%\n bucket 11: 40%\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 bucket 11: 90%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 13 of 60\n Reserving size (126) 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%\nGetting block 14 of 60\n Sorting block of length 85 for bucket 13\n Reserving size (126) for bucket 14\n (Using difference cover)\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 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) 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 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n Entering block accumulator loop for bucket 17:\n bucket 16: 20%\n bucket 17: 10%\n bucket 16: 30%\n bucket 17: 20%\n bucket 16: 40%\n bucket 17: 30%\n bucket 16: 50%\n bucket 17: 40%\n bucket 16: 60%\n bucket 17: 50%\n bucket 16: 70%\n bucket 17: 60%\n bucket 16: 80%\n bucket 17: 70%\n bucket 16: 90%\n bucket 17: 80%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n bucket 17: 90%\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Entering block accumulator loop for bucket 18:\n Calculating Z arrays for bucket 19\n bucket 18: 10%\n Entering block accumulator loop for bucket 19:\n bucket 18: 20%\n bucket 19: 10%\n bucket 18: 30%\n bucket 19: 20%\n bucket 18: 40%\n bucket 19: 30%\n bucket 18: 50%\n bucket 19: 40%\n bucket 18: 60%\n bucket 19: 50%\n bucket 18: 70%\n bucket 19: 60%\n bucket 18: 80%\n bucket 19: 70%\n bucket 18: 90%\n bucket 19: 80%\n bucket 18: 100%\n bucket 19: 90%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\n Entering block accumulator loop for bucket 21:\n bucket 20: 10%\n bucket 21: 10%\n bucket 20: 20%\n bucket 21: 20%\n bucket 20: 30%\n bucket 21: 30%\n bucket 20: 40%\n bucket 21: 40%\n bucket 20: 50%\n bucket 21: 50%\n bucket 20: 60%\n bucket 21: 60%\n bucket 20: 70%\n bucket 21: 70%\n bucket 20: 80%\n bucket 21: 80%\n bucket 20: 90%\n bucket 21: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) 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 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n bucket 22: 50%\n bucket 23: 20%\n bucket 22: 60%\n bucket 23: 30%\n bucket 22: 70%\n bucket 23: 40%\n bucket 22: 80%\n bucket 22: 90%\n bucket 23: 50%\n bucket 22: 100%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\n Reserving size (126) 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 60\n bucket 24: 20%\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 30%\n bucket 24: 40%\n Entering block accumulator loop for bucket 25:\n bucket 24: 50%\n bucket 25: 10%\n bucket 24: 60%\n bucket 25: 20%\n bucket 24: 70%\n bucket 24: 80%\n bucket 25: 30%\n bucket 24: 90%\n bucket 25: 40%\n bucket 24: 100%\n bucket 25: 50%\n Sorting block of length 68 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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\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 Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) 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 106 for bucket 28\n (Using difference cover)\nGetting block 29 of 60\n Sorting block time: 00:00:00\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nReturning block of 107 for bucket 28\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 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\nGetting block 32 of 60\n bucket 31: 90%\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\n bucket 32: 40%\n bucket 32: 50%\n bucket 32: 60%\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\nGetting block 34 of 60\n bucket 33: 30%\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 40%\n bucket 33: 50%\n Entering block accumulator loop for bucket 34:\n bucket 33: 60%\n bucket 33: 70%\n bucket 34: 10%\n bucket 33: 80%\n bucket 33: 90%\n bucket 34: 20%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\nGetting block 37 of 60\n bucket 36: 50%\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 60%\n bucket 36: 70%\n Entering block accumulator loop for bucket 37:\n bucket 36: 80%\n bucket 36: 90%\n bucket 37: 10%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\nGetting block 39 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 39:\n bucket 38: 10%\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 39: 20%\n bucket 38: 40%\n bucket 38: 50%\n bucket 39: 30%\n bucket 38: 60%\n bucket 39: 40%\n bucket 38: 70%\n bucket 39: 50%\n bucket 38: 80%\n bucket 38: 90%\n bucket 39: 60%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 42:\n bucket 41: 10%\n bucket 41: 20%\n bucket 42: 10%\n bucket 41: 30%\n bucket 42: 20%\n bucket 41: 40%\n bucket 42: 30%\n bucket 41: 50%\n bucket 42: 40%\n bucket 41: 60%\n bucket 42: 50%\n bucket 41: 70%\n bucket 42: 60%\n bucket 41: 80%\n bucket 42: 70%\n bucket 41: 90%\n bucket 42: 80%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Entering block accumulator loop for bucket 43:\n Calculating Z arrays for bucket 44\n bucket 43: 10%\n bucket 43: 20%\n Entering block accumulator loop for bucket 44:\n bucket 43: 30%\n bucket 44: 10%\n bucket 43: 40%\n bucket 44: 20%\n bucket 43: 50%\n bucket 44: 30%\n bucket 43: 60%\n bucket 44: 40%\n bucket 43: 70%\n bucket 44: 50%\n bucket 43: 80%\n bucket 44: 60%\n bucket 43: 90%\n bucket 44: 70%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\nGetting block 47 of 60\n bucket 46: 60%\n bucket 46: 70%\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 80%\n bucket 46: 90%\n Entering block accumulator loop for bucket 47:\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 60\n Entering block accumulator loop for bucket 50:\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 10%\n Entering block accumulator loop for bucket 51:\n bucket 50: 20%\n bucket 51: 10%\n bucket 51: 20%\n bucket 50: 30%\n bucket 51: 30%\n bucket 50: 40%\n bucket 51: 40%\n bucket 50: 50%\n bucket 51: 50%\n bucket 51: 60%\n bucket 50: 60%\n bucket 51: 70%\n bucket 50: 70%\n bucket 51: 80%\n bucket 50: 80%\n bucket 51: 90%\n bucket 51: 100%\n bucket 50: 90%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\nGetting block 53 of 60\n bucket 52: 40%\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 50%\n bucket 52: 60%\n Entering block accumulator loop for bucket 53:\n bucket 52: 70%\n bucket 53: 10%\n bucket 52: 80%\n bucket 53: 20%\n bucket 52: 90%\n bucket 53: 30%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n bucket 53: 40%\n (Using difference cover)\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 50%\n bucket 56: 60%\n Entering block accumulator loop for bucket 57:\n bucket 56: 70%\n bucket 57: 10%\n bucket 56: 80%\n bucket 57: 20%\n bucket 56: 90%\n bucket 57: 30%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n Entering block accumulator loop for bucket 59:\n bucket 58: 80%\n bucket 59: 10%\n bucket 58: 90%\n bucket 58: 100%\n bucket 59: 20%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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\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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 2 of 60\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Reserving size (126) for bucket 2\nGetting block 3 of 60\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\nGetting block 4 of 60\nGetting block 5 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 4\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 4\n Reserving size (126) for bucket 5\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 5\nGetting block 7 of 60\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 7\n bucket 4: 10%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 5:\nGetting block 8 of 60\n bucket 4: 20%\n bucket 5: 10%\n Calculating Z arrays for bucket 7\n bucket 1: 20%\n bucket 2: 10%\n bucket 5: 20%\n bucket 1: 30%\n Entering block accumulator loop for bucket 3:\n Reserving size (126) for bucket 8\n bucket 5: 30%\n Entering block accumulator loop for bucket 7:\n bucket 2: 20%\n bucket 5: 40%\n bucket 4: 30%\n bucket 7: 10%\n Calculating Z arrays for bucket 8\n bucket 2: 30%\n bucket 5: 50%\n bucket 1: 40%\n bucket 4: 40%\n bucket 3: 10%\n bucket 4: 50%\n bucket 5: 60%\n bucket 7: 20%\n Entering block accumulator loop for bucket 8:\n bucket 2: 40%\n bucket 3: 20%\n bucket 1: 50%\n bucket 7: 30%\n bucket 4: 60%\n bucket 6: 10%\n bucket 2: 50%\n bucket 4: 70%\n bucket 1: 60%\n bucket 7: 40%\n bucket 8: 10%\n bucket 3: 30%\n bucket 7: 50%\n bucket 2: 60%\n bucket 8: 20%\n bucket 6: 20%\n bucket 1: 70%\n bucket 4: 80%\n bucket 7: 60%\n bucket 2: 70%\n bucket 5: 70%\n bucket 1: 80%\n bucket 4: 90%\n bucket 8: 30%\n bucket 5: 80%\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 1: 90%\n bucket 7: 70%\n bucket 6: 30%\n bucket 1: 100%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 7: 80%\n bucket 8: 40%\n bucket 5: 90%\n bucket 7: 90%\n bucket 2: 80%\n bucket 6: 40%\n bucket 5: 100%\n bucket 7: 100%\n bucket 2: 90%\n bucket 3: 40%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 50%\n bucket 2: 100%\n bucket 3: 50%\n bucket 6: 50%\n bucket 8: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 6: 60%\n bucket 3: 60%\n Sorting block of length 75 for bucket 7\n bucket 6: 70%\n (Using difference cover)\n bucket 8: 70%\n bucket 6: 80%\n bucket 3: 70%\n bucket 8: 80%\n bucket 6: 90%\n bucket 3: 80%\n bucket 8: 90%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 3: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 3: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) 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%\nGetting block 10 of 60\n bucket 9: 80%\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 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 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n Entering block accumulator loop for bucket 11:\n bucket 12: 30%\n bucket 11: 10%\n bucket 12: 40%\n bucket 11: 20%\n bucket 12: 50%\n bucket 11: 30%\n bucket 12: 60%\n bucket 11: 40%\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 bucket 11: 90%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 13 of 60\n Reserving size (126) 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%\nGetting block 14 of 60\n Sorting block of length 85 for bucket 13\n Reserving size (126) for bucket 14\n (Using difference cover)\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 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) 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 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n Entering block accumulator loop for bucket 17:\n bucket 16: 20%\n bucket 17: 10%\n bucket 16: 30%\n bucket 17: 20%\n bucket 16: 40%\n bucket 17: 30%\n bucket 16: 50%\n bucket 17: 40%\n bucket 16: 60%\n bucket 17: 50%\n bucket 16: 70%\n bucket 17: 60%\n bucket 16: 80%\n bucket 17: 70%\n bucket 16: 90%\n bucket 17: 80%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n bucket 17: 90%\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Entering block accumulator loop for bucket 18:\n Calculating Z arrays for bucket 19\n bucket 18: 10%\n Entering block accumulator loop for bucket 19:\n bucket 18: 20%\n bucket 19: 10%\n bucket 18: 30%\n bucket 19: 20%\n bucket 18: 40%\n bucket 19: 30%\n bucket 18: 50%\n bucket 19: 40%\n bucket 18: 60%\n bucket 19: 50%\n bucket 18: 70%\n bucket 19: 60%\n bucket 18: 80%\n bucket 19: 70%\n bucket 18: 90%\n bucket 19: 80%\n bucket 18: 100%\n bucket 19: 90%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\n Entering block accumulator loop for bucket 21:\n bucket 20: 10%\n bucket 21: 10%\n bucket 20: 20%\n bucket 21: 20%\n bucket 20: 30%\n bucket 21: 30%\n bucket 20: 40%\n bucket 21: 40%\n bucket 20: 50%\n bucket 21: 50%\n bucket 20: 60%\n bucket 21: 60%\n bucket 20: 70%\n bucket 21: 70%\n bucket 20: 80%\n bucket 21: 80%\n bucket 20: 90%\n bucket 21: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) 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 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n bucket 22: 50%\n bucket 23: 20%\n bucket 22: 60%\n bucket 23: 30%\n bucket 22: 70%\n bucket 23: 40%\n bucket 22: 80%\n bucket 22: 90%\n bucket 23: 50%\n bucket 22: 100%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\n Reserving size (126) 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 60\n bucket 24: 20%\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 30%\n bucket 24: 40%\n Entering block accumulator loop for bucket 25:\n bucket 24: 50%\n bucket 25: 10%\n bucket 24: 60%\n bucket 25: 20%\n bucket 24: 70%\n bucket 24: 80%\n bucket 25: 30%\n bucket 24: 90%\n bucket 25: 40%\n bucket 24: 100%\n bucket 25: 50%\n Sorting block of length 68 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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\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 Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) 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 106 for bucket 28\n (Using difference cover)\nGetting block 29 of 60\n Sorting block time: 00:00:00\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nReturning block of 107 for bucket 28\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 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\nGetting block 32 of 60\n bucket 31: 90%\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\n bucket 32: 40%\n bucket 32: 50%\n bucket 32: 60%\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\nGetting block 34 of 60\n bucket 33: 30%\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 40%\n bucket 33: 50%\n Entering block accumulator loop for bucket 34:\n bucket 33: 60%\n bucket 33: 70%\n bucket 34: 10%\n bucket 33: 80%\n bucket 33: 90%\n bucket 34: 20%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\nGetting block 37 of 60\n bucket 36: 50%\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 60%\n bucket 36: 70%\n Entering block accumulator loop for bucket 37:\n bucket 36: 80%\n bucket 36: 90%\n bucket 37: 10%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\nGetting block 39 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 39:\n bucket 38: 10%\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 39: 20%\n bucket 38: 40%\n bucket 38: 50%\n bucket 39: 30%\n bucket 38: 60%\n bucket 39: 40%\n bucket 38: 70%\n bucket 39: 50%\n bucket 38: 80%\n bucket 38: 90%\n bucket 39: 60%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 42:\n bucket 41: 10%\n bucket 41: 20%\n bucket 42: 10%\n bucket 41: 30%\n bucket 42: 20%\n bucket 41: 40%\n bucket 42: 30%\n bucket 41: 50%\n bucket 42: 40%\n bucket 41: 60%\n bucket 42: 50%\n bucket 41: 70%\n bucket 42: 60%\n bucket 41: 80%\n bucket 42: 70%\n bucket 41: 90%\n bucket 42: 80%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Entering block accumulator loop for bucket 43:\n Calculating Z arrays for bucket 44\n bucket 43: 10%\n bucket 43: 20%\n Entering block accumulator loop for bucket 44:\n bucket 43: 30%\n bucket 44: 10%\n bucket 43: 40%\n bucket 44: 20%\n bucket 43: 50%\n bucket 44: 30%\n bucket 43: 60%\n bucket 44: 40%\n bucket 43: 70%\n bucket 44: 50%\n bucket 43: 80%\n bucket 44: 60%\n bucket 43: 90%\n bucket 44: 70%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\nGetting block 47 of 60\n bucket 46: 60%\n bucket 46: 70%\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 80%\n bucket 46: 90%\n Entering block accumulator loop for bucket 47:\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 60\n Entering block accumulator loop for bucket 50:\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 10%\n Entering block accumulator loop for bucket 51:\n bucket 50: 20%\n bucket 51: 10%\n bucket 51: 20%\n bucket 50: 30%\n bucket 51: 30%\n bucket 50: 40%\n bucket 51: 40%\n bucket 50: 50%\n bucket 51: 50%\n bucket 51: 60%\n bucket 50: 60%\n bucket 51: 70%\n bucket 50: 70%\n bucket 51: 80%\n bucket 50: 80%\n bucket 51: 90%\n bucket 51: 100%\n bucket 50: 90%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\nGetting block 53 of 60\n bucket 52: 40%\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 50%\n bucket 52: 60%\n Entering block accumulator loop for bucket 53:\n bucket 52: 70%\n bucket 53: 10%\n bucket 52: 80%\n bucket 53: 20%\n bucket 52: 90%\n bucket 53: 30%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n bucket 53: 40%\n (Using difference cover)\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 50%\n bucket 56: 60%\n Entering block accumulator loop for bucket 57:\n bucket 56: 70%\n bucket 57: 10%\n bucket 56: 80%\n bucket 57: 20%\n bucket 56: 90%\n bucket 57: 30%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n Entering block accumulator loop for bucket 59:\n bucket 58: 80%\n bucket 59: 10%\n bucket 58: 90%\n bucket 58: 100%\n bucket 59: 20%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:39:29", "plugin": "core", "name": "end_epoch", "raw_value": "1736861969.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:39:28", "plugin": "core", "name": "start_epoch", "raw_value": "1736861968.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 30.620455741882324, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "afcf8871ec603619"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "86ece21faece569d"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "e1bbba116b2d216c", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:40:09.564918", "create_time": "2025-01-14T13:39:56.795219", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-8pf6r", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/7/1/6/dataset_71660eee-be48-4194-b17a-eafb1a0b6263.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/e/8/b/dataset_e8b1ff23-b9e9-4267-8155-05ebc374c185.dat' > input_f.fastq && seqtk seq -2 '/galaxy/server/database/objects/e/8/b/dataset_e8b1ff23-b9e9-4267-8155-05ebc374c185.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/2/2/4/dataset_224145e3-0b11-4fd3-9ceb-5ed9d3d5ceff.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\": 241, \"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\": 240, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "afcf8871ec603619", "src": "hda", "uuid": "71660eee-be48-4194-b17a-eafb1a0b6263"}, "library|input_1": {"id": "86ece21faece569d", "src": "hda", "uuid": "e8b1ff23-b9e9-4267-8155-05ebc374c185"}}, "outputs": {"output_alignments": {"id": "99d66cb71c7ef74f", "src": "hda", "uuid": "224145e3-0b11-4fd3-9ceb-5ed9d3d5ceff"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\nGetting block 3 of 60\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Reserving size (126) for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 2:\nGetting block 5 of 60\nGetting block 6 of 60\n Reserving size (126) for bucket 6\nGetting block 7 of 60\n Calculating Z arrays for bucket 6\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 2: 10%\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 8\n bucket 1: 20%\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 6:\n Reserving size (126) for bucket 5\n bucket 6: 10%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 8:\n Calculating Z arrays for bucket 7\n bucket 4: 10%\n Entering block accumulator loop for bucket 3:\n bucket 6: 20%\n bucket 1: 30%\n bucket 2: 20%\n Entering block accumulator loop for bucket 7:\n bucket 8: 10%\n bucket 2: 30%\n bucket 4: 20%\n bucket 7: 10%\n bucket 1: 40%\n bucket 6: 30%\n bucket 2: 40%\n bucket 1: 50%\n bucket 4: 30%\n bucket 6: 40%\n Calculating Z arrays for bucket 5\n bucket 4: 40%\n bucket 2: 50%\n bucket 8: 20%\n bucket 7: 20%\n bucket 1: 60%\n bucket 6: 50%\n bucket 3: 10%\n bucket 1: 70%\n Entering block accumulator loop for bucket 5:\n bucket 2: 60%\n bucket 7: 30%\n bucket 8: 30%\n bucket 6: 60%\n bucket 3: 20%\n bucket 5: 10%\n bucket 6: 70%\n bucket 3: 30%\n bucket 8: 40%\n bucket 2: 70%\n bucket 1: 80%\n bucket 8: 50%\n bucket 6: 80%\n bucket 7: 40%\n bucket 1: 90%\n bucket 8: 60%\n bucket 6: 90%\n bucket 7: 50%\n bucket 2: 80%\n bucket 3: 40%\n bucket 5: 20%\n bucket 6: 100%\n bucket 2: 90%\n bucket 1: 100%\n bucket 4: 50%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 8: 70%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 2: 100%\n bucket 5: 30%\n bucket 3: 50%\n bucket 4: 60%\n bucket 5: 40%\n Sorting block of length 84 for bucket 2\n bucket 3: 60%\n bucket 5: 50%\n bucket 4: 70%\n bucket 7: 60%\n (Using difference cover)\n bucket 5: 60%\n bucket 8: 80%\n bucket 4: 80%\n bucket 7: 70%\n bucket 3: 70%\n bucket 5: 70%\n bucket 8: 90%\n bucket 3: 80%\n bucket 7: 80%\n bucket 5: 80%\n bucket 8: 100%\n bucket 4: 90%\n bucket 3: 90%\n bucket 7: 90%\n bucket 4: 100%\n Sorting block of length 94 for bucket 8\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n (Using difference cover)\n bucket 3: 100%\n bucket 7: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 5: 90%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\nGetting block 10 of 60\n Reserving size (126) for bucket 9\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n Entering block accumulator loop for bucket 9:\n bucket 10: 20%\n bucket 10: 30%\n bucket 9: 10%\n bucket 10: 40%\n bucket 9: 20%\n bucket 10: 50%\n bucket 9: 30%\n bucket 10: 60%\n bucket 10: 70%\n bucket 9: 40%\n bucket 10: 80%\n bucket 9: 50%\n bucket 10: 90%\n bucket 9: 60%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Reserving size (126) 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 95 for bucket 11\n (Using difference cover)\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 13 of 60\n Reserving size (126) 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%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n Entering block accumulator loop for bucket 14:\n bucket 13: 60%\n bucket 14: 10%\n bucket 13: 70%\n bucket 14: 20%\n bucket 13: 80%\n bucket 14: 30%\n bucket 13: 90%\n bucket 14: 40%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\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 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) 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%\nGetting block 16 of 60\n bucket 15: 30%\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n Entering block accumulator loop for bucket 16:\n bucket 15: 70%\n bucket 16: 10%\n bucket 15: 80%\n bucket 16: 20%\n bucket 15: 90%\n bucket 16: 30%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\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 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 18:\n Entering block accumulator loop for bucket 17:\n bucket 18: 10%\n bucket 17: 10%\n bucket 18: 20%\n bucket 17: 20%\n bucket 18: 30%\n bucket 17: 30%\n bucket 18: 40%\n bucket 17: 40%\n bucket 18: 50%\n bucket 17: 50%\n bucket 18: 60%\n bucket 17: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 17: 70%\n bucket 18: 90%\n bucket 17: 80%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 19 of 60\n Reserving size (126) 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%\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 30%\n bucket 19: 40%\n Entering block accumulator loop for bucket 20:\n bucket 19: 50%\n bucket 20: 10%\n bucket 19: 60%\n bucket 20: 20%\n bucket 19: 70%\n bucket 20: 30%\n bucket 19: 80%\n bucket 20: 40%\n bucket 19: 90%\n bucket 20: 50%\n bucket 19: 100%\n bucket 20: 60%\n Sorting block of length 107 for bucket 19\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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Entering block accumulator loop for bucket 21:\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 10%\n bucket 21: 20%\n Entering block accumulator loop for bucket 22:\n bucket 21: 30%\n bucket 21: 40%\n bucket 22: 10%\n bucket 21: 50%\n bucket 21: 60%\n bucket 22: 20%\n bucket 21: 70%\n bucket 22: 30%\n bucket 21: 80%\n bucket 22: 40%\n bucket 21: 90%\n bucket 22: 50%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\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 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 23: 30%\n bucket 24: 10%\n bucket 23: 40%\n bucket 24: 20%\n bucket 23: 50%\n bucket 24: 30%\n bucket 23: 60%\n bucket 23: 70%\n bucket 24: 40%\n bucket 23: 80%\n bucket 24: 50%\n bucket 23: 90%\n bucket 24: 60%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) 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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Entering block accumulator loop for bucket 26:\n Reserving size (126) 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 27: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) 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%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 70%\n bucket 28: 80%\n Entering block accumulator loop for bucket 29:\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\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 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 10%\n bucket 31: 20%\n Entering block accumulator loop for bucket 32:\n bucket 31: 30%\n bucket 32: 10%\n bucket 31: 40%\n bucket 32: 20%\n bucket 31: 50%\n bucket 32: 30%\n bucket 31: 60%\n bucket 32: 40%\n bucket 31: 70%\n bucket 32: 50%\n bucket 31: 80%\n bucket 32: 60%\n bucket 31: 90%\n bucket 31: 100%\n bucket 32: 70%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\nGetting block 34 of 60\n bucket 33: 10%\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 20%\n Entering block accumulator loop for bucket 34:\n bucket 33: 30%\n bucket 34: 10%\n bucket 33: 40%\n bucket 34: 20%\n bucket 33: 50%\n bucket 34: 30%\n bucket 33: 60%\n bucket 34: 40%\n bucket 34: 50%\n bucket 33: 70%\n bucket 34: 60%\n bucket 33: 80%\n bucket 34: 70%\n bucket 33: 90%\n bucket 34: 80%\n bucket 34: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n bucket 34: 100%\n (Using difference cover)\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n Entering block accumulator loop for bucket 39:\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 38: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 38: 50%\n bucket 39: 70%\n bucket 39: 80%\n bucket 38: 60%\n bucket 39: 90%\n bucket 38: 70%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\nGetting block 42 of 60\n Reserving size (126) for bucket 41\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 41\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 41: 10%\n bucket 42: 20%\n bucket 41: 20%\n bucket 42: 30%\n bucket 41: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 41: 40%\n bucket 42: 60%\n bucket 41: 50%\n bucket 42: 70%\n bucket 41: 60%\n bucket 42: 80%\n bucket 41: 70%\n bucket 42: 90%\n bucket 41: 80%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\nGetting block 44 of 60\n bucket 43: 10%\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n bucket 43: 20%\n bucket 43: 30%\n Entering block accumulator loop for bucket 44:\n bucket 43: 40%\n bucket 44: 10%\n bucket 43: 50%\n bucket 44: 20%\n bucket 43: 60%\n bucket 44: 30%\n bucket 43: 70%\n bucket 43: 80%\n bucket 44: 40%\n bucket 43: 90%\n bucket 44: 50%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Entering block accumulator loop for bucket 46:\n Calculating Z arrays for bucket 47\n bucket 46: 10%\n bucket 46: 20%\n Entering block accumulator loop for bucket 47:\n bucket 46: 30%\n bucket 47: 10%\n bucket 46: 40%\n bucket 47: 20%\n bucket 46: 50%\n bucket 47: 30%\n bucket 46: 60%\n bucket 47: 40%\n bucket 46: 70%\n bucket 47: 50%\n bucket 46: 80%\n bucket 47: 60%\n bucket 46: 90%\n bucket 47: 70%\n bucket 46: 100%\n bucket 47: 80%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n bucket 48: 70%\n Calculating Z arrays for bucket 49\n bucket 48: 80%\n bucket 48: 90%\n Entering block accumulator loop for bucket 49:\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n Entering block accumulator loop for bucket 52:\n bucket 51: 20%\n bucket 51: 30%\n bucket 52: 10%\n bucket 51: 40%\n bucket 52: 20%\n bucket 51: 50%\n bucket 52: 30%\n bucket 51: 60%\n bucket 52: 40%\n bucket 51: 70%\n bucket 52: 50%\n bucket 51: 80%\n bucket 51: 90%\n bucket 52: 60%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\nGetting block 54 of 60\n bucket 53: 20%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n Entering block accumulator loop for bucket 54:\n bucket 53: 60%\n bucket 54: 10%\n bucket 53: 70%\n bucket 53: 80%\n bucket 54: 20%\n bucket 53: 90%\n bucket 54: 30%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n Entering block accumulator loop for bucket 57:\n bucket 56: 20%\n bucket 57: 10%\n bucket 56: 30%\n bucket 56: 40%\n bucket 57: 20%\n bucket 56: 50%\n bucket 56: 60%\n bucket 57: 30%\n bucket 56: 70%\n bucket 57: 40%\n bucket 56: 80%\n bucket 56: 90%\n bucket 57: 50%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 58:\n Entering block accumulator loop for bucket 59:\n bucket 58: 10%\n bucket 59: 10%\n bucket 58: 20%\n bucket 59: 20%\n bucket 59: 30%\n bucket 58: 30%\n bucket 59: 40%\n bucket 58: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 58: 50%\n bucket 59: 70%\n bucket 58: 60%\n bucket 59: 80%\n bucket 58: 70%\n bucket 59: 90%\n bucket 59: 100%\n bucket 58: 80%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\nGetting block 3 of 60\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Reserving size (126) for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 2:\nGetting block 5 of 60\nGetting block 6 of 60\n Reserving size (126) for bucket 6\nGetting block 7 of 60\n Calculating Z arrays for bucket 6\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 2: 10%\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 8\n bucket 1: 20%\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 6:\n Reserving size (126) for bucket 5\n bucket 6: 10%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 8:\n Calculating Z arrays for bucket 7\n bucket 4: 10%\n Entering block accumulator loop for bucket 3:\n bucket 6: 20%\n bucket 1: 30%\n bucket 2: 20%\n Entering block accumulator loop for bucket 7:\n bucket 8: 10%\n bucket 2: 30%\n bucket 4: 20%\n bucket 7: 10%\n bucket 1: 40%\n bucket 6: 30%\n bucket 2: 40%\n bucket 1: 50%\n bucket 4: 30%\n bucket 6: 40%\n Calculating Z arrays for bucket 5\n bucket 4: 40%\n bucket 2: 50%\n bucket 8: 20%\n bucket 7: 20%\n bucket 1: 60%\n bucket 6: 50%\n bucket 3: 10%\n bucket 1: 70%\n Entering block accumulator loop for bucket 5:\n bucket 2: 60%\n bucket 7: 30%\n bucket 8: 30%\n bucket 6: 60%\n bucket 3: 20%\n bucket 5: 10%\n bucket 6: 70%\n bucket 3: 30%\n bucket 8: 40%\n bucket 2: 70%\n bucket 1: 80%\n bucket 8: 50%\n bucket 6: 80%\n bucket 7: 40%\n bucket 1: 90%\n bucket 8: 60%\n bucket 6: 90%\n bucket 7: 50%\n bucket 2: 80%\n bucket 3: 40%\n bucket 5: 20%\n bucket 6: 100%\n bucket 2: 90%\n bucket 1: 100%\n bucket 4: 50%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 8: 70%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 2: 100%\n bucket 5: 30%\n bucket 3: 50%\n bucket 4: 60%\n bucket 5: 40%\n Sorting block of length 84 for bucket 2\n bucket 3: 60%\n bucket 5: 50%\n bucket 4: 70%\n bucket 7: 60%\n (Using difference cover)\n bucket 5: 60%\n bucket 8: 80%\n bucket 4: 80%\n bucket 7: 70%\n bucket 3: 70%\n bucket 5: 70%\n bucket 8: 90%\n bucket 3: 80%\n bucket 7: 80%\n bucket 5: 80%\n bucket 8: 100%\n bucket 4: 90%\n bucket 3: 90%\n bucket 7: 90%\n bucket 4: 100%\n Sorting block of length 94 for bucket 8\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n (Using difference cover)\n bucket 3: 100%\n bucket 7: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 5: 90%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\nGetting block 10 of 60\n Reserving size (126) for bucket 9\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n Entering block accumulator loop for bucket 9:\n bucket 10: 20%\n bucket 10: 30%\n bucket 9: 10%\n bucket 10: 40%\n bucket 9: 20%\n bucket 10: 50%\n bucket 9: 30%\n bucket 10: 60%\n bucket 10: 70%\n bucket 9: 40%\n bucket 10: 80%\n bucket 9: 50%\n bucket 10: 90%\n bucket 9: 60%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Reserving size (126) 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 95 for bucket 11\n (Using difference cover)\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 13 of 60\n Reserving size (126) 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%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n Entering block accumulator loop for bucket 14:\n bucket 13: 60%\n bucket 14: 10%\n bucket 13: 70%\n bucket 14: 20%\n bucket 13: 80%\n bucket 14: 30%\n bucket 13: 90%\n bucket 14: 40%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\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 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) 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%\nGetting block 16 of 60\n bucket 15: 30%\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n Entering block accumulator loop for bucket 16:\n bucket 15: 70%\n bucket 16: 10%\n bucket 15: 80%\n bucket 16: 20%\n bucket 15: 90%\n bucket 16: 30%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\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 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 18:\n Entering block accumulator loop for bucket 17:\n bucket 18: 10%\n bucket 17: 10%\n bucket 18: 20%\n bucket 17: 20%\n bucket 18: 30%\n bucket 17: 30%\n bucket 18: 40%\n bucket 17: 40%\n bucket 18: 50%\n bucket 17: 50%\n bucket 18: 60%\n bucket 17: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 17: 70%\n bucket 18: 90%\n bucket 17: 80%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 19 of 60\n Reserving size (126) 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%\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 30%\n bucket 19: 40%\n Entering block accumulator loop for bucket 20:\n bucket 19: 50%\n bucket 20: 10%\n bucket 19: 60%\n bucket 20: 20%\n bucket 19: 70%\n bucket 20: 30%\n bucket 19: 80%\n bucket 20: 40%\n bucket 19: 90%\n bucket 20: 50%\n bucket 19: 100%\n bucket 20: 60%\n Sorting block of length 107 for bucket 19\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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Entering block accumulator loop for bucket 21:\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 10%\n bucket 21: 20%\n Entering block accumulator loop for bucket 22:\n bucket 21: 30%\n bucket 21: 40%\n bucket 22: 10%\n bucket 21: 50%\n bucket 21: 60%\n bucket 22: 20%\n bucket 21: 70%\n bucket 22: 30%\n bucket 21: 80%\n bucket 22: 40%\n bucket 21: 90%\n bucket 22: 50%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\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 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 23: 30%\n bucket 24: 10%\n bucket 23: 40%\n bucket 24: 20%\n bucket 23: 50%\n bucket 24: 30%\n bucket 23: 60%\n bucket 23: 70%\n bucket 24: 40%\n bucket 23: 80%\n bucket 24: 50%\n bucket 23: 90%\n bucket 24: 60%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) 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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Entering block accumulator loop for bucket 26:\n Reserving size (126) 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 27: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) 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%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 70%\n bucket 28: 80%\n Entering block accumulator loop for bucket 29:\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\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 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 10%\n bucket 31: 20%\n Entering block accumulator loop for bucket 32:\n bucket 31: 30%\n bucket 32: 10%\n bucket 31: 40%\n bucket 32: 20%\n bucket 31: 50%\n bucket 32: 30%\n bucket 31: 60%\n bucket 32: 40%\n bucket 31: 70%\n bucket 32: 50%\n bucket 31: 80%\n bucket 32: 60%\n bucket 31: 90%\n bucket 31: 100%\n bucket 32: 70%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\nGetting block 34 of 60\n bucket 33: 10%\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 20%\n Entering block accumulator loop for bucket 34:\n bucket 33: 30%\n bucket 34: 10%\n bucket 33: 40%\n bucket 34: 20%\n bucket 33: 50%\n bucket 34: 30%\n bucket 33: 60%\n bucket 34: 40%\n bucket 34: 50%\n bucket 33: 70%\n bucket 34: 60%\n bucket 33: 80%\n bucket 34: 70%\n bucket 33: 90%\n bucket 34: 80%\n bucket 34: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n bucket 34: 100%\n (Using difference cover)\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n Entering block accumulator loop for bucket 39:\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 38: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 38: 50%\n bucket 39: 70%\n bucket 39: 80%\n bucket 38: 60%\n bucket 39: 90%\n bucket 38: 70%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\nGetting block 42 of 60\n Reserving size (126) for bucket 41\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 41\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 41: 10%\n bucket 42: 20%\n bucket 41: 20%\n bucket 42: 30%\n bucket 41: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 41: 40%\n bucket 42: 60%\n bucket 41: 50%\n bucket 42: 70%\n bucket 41: 60%\n bucket 42: 80%\n bucket 41: 70%\n bucket 42: 90%\n bucket 41: 80%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\nGetting block 44 of 60\n bucket 43: 10%\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n bucket 43: 20%\n bucket 43: 30%\n Entering block accumulator loop for bucket 44:\n bucket 43: 40%\n bucket 44: 10%\n bucket 43: 50%\n bucket 44: 20%\n bucket 43: 60%\n bucket 44: 30%\n bucket 43: 70%\n bucket 43: 80%\n bucket 44: 40%\n bucket 43: 90%\n bucket 44: 50%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Entering block accumulator loop for bucket 46:\n Calculating Z arrays for bucket 47\n bucket 46: 10%\n bucket 46: 20%\n Entering block accumulator loop for bucket 47:\n bucket 46: 30%\n bucket 47: 10%\n bucket 46: 40%\n bucket 47: 20%\n bucket 46: 50%\n bucket 47: 30%\n bucket 46: 60%\n bucket 47: 40%\n bucket 46: 70%\n bucket 47: 50%\n bucket 46: 80%\n bucket 47: 60%\n bucket 46: 90%\n bucket 47: 70%\n bucket 46: 100%\n bucket 47: 80%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n bucket 48: 70%\n Calculating Z arrays for bucket 49\n bucket 48: 80%\n bucket 48: 90%\n Entering block accumulator loop for bucket 49:\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n Entering block accumulator loop for bucket 52:\n bucket 51: 20%\n bucket 51: 30%\n bucket 52: 10%\n bucket 51: 40%\n bucket 52: 20%\n bucket 51: 50%\n bucket 52: 30%\n bucket 51: 60%\n bucket 52: 40%\n bucket 51: 70%\n bucket 52: 50%\n bucket 51: 80%\n bucket 51: 90%\n bucket 52: 60%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\nGetting block 54 of 60\n bucket 53: 20%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n Entering block accumulator loop for bucket 54:\n bucket 53: 60%\n bucket 54: 10%\n bucket 53: 70%\n bucket 53: 80%\n bucket 54: 20%\n bucket 53: 90%\n bucket 54: 30%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n Entering block accumulator loop for bucket 57:\n bucket 56: 20%\n bucket 57: 10%\n bucket 56: 30%\n bucket 56: 40%\n bucket 57: 20%\n bucket 56: 50%\n bucket 56: 60%\n bucket 57: 30%\n bucket 56: 70%\n bucket 57: 40%\n bucket 56: 80%\n bucket 56: 90%\n bucket 57: 50%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 58:\n Entering block accumulator loop for bucket 59:\n bucket 58: 10%\n bucket 59: 10%\n bucket 58: 20%\n bucket 59: 20%\n bucket 59: 30%\n bucket 58: 30%\n bucket 59: 40%\n bucket 58: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 58: 50%\n bucket 59: 70%\n bucket 58: 60%\n bucket 59: 80%\n bucket 58: 70%\n bucket 59: 90%\n bucket 59: 100%\n bucket 58: 80%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:39:59", "plugin": "core", "name": "end_epoch", "raw_value": "1736861999.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:39:58", "plugin": "core", "name": "start_epoch", "raw_value": "1736861998.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 29.468528985977173, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "985d5e22a7b4af9d"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "b84e37f287448d2d"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "28a769a7a9fbe219", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:40:39.283421", "create_time": "2025-01-14T13:40:28.025033", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-wxmfg", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/1/2/d/dataset_12d1e486-b7ae-457c-bab3-5f5a0e40c42d.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && bzcat '/galaxy/server/database/objects/d/6/c/dataset_d6c48fe7-2215-4c9f-8011-2beeeb127177.dat' | seqtk seq -1 /dev/stdin > input_f.fastq && bzcat '/galaxy/server/database/objects/d/6/c/dataset_d6c48fe7-2215-4c9f-8011-2beeeb127177.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/4/4/b/dataset_44be467e-43ec-4958-b518-1ce13cdfab41.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\": 244, \"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\": 243, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "985d5e22a7b4af9d", "src": "hda", "uuid": "12d1e486-b7ae-457c-bab3-5f5a0e40c42d"}, "library|input_1": {"id": "b84e37f287448d2d", "src": "hda", "uuid": "d6c48fe7-2215-4c9f-8011-2beeeb127177"}}, "outputs": {"output_alignments": {"id": "c10899d5abb8a30a", "src": "hda", "uuid": "44be467e-43ec-4958-b518-1ce13cdfab41"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\nGetting block 3 of 60\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 3\nGetting block 4 of 60\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n Entering block accumulator loop for bucket 2:\n bucket 1: 10%\n Reserving size (126) for bucket 4\nGetting block 6 of 60\n Calculating Z arrays for bucket 3\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n Calculating Z arrays for bucket 4\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 7\n bucket 2: 10%\n Calculating Z arrays for bucket 6\n bucket 1: 20%\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 7:\n bucket 4: 10%\n Entering block accumulator loop for bucket 6:\n bucket 2: 20%\n Calculating Z arrays for bucket 5\n bucket 6: 10%\n Entering block accumulator loop for bucket 3:\n bucket 4: 20%\n bucket 1: 30%\n bucket 2: 30%\n bucket 6: 20%\n bucket 3: 10%\n bucket 2: 40%\n bucket 4: 30%\n bucket 1: 40%\n bucket 7: 10%\n bucket 3: 20%\n Entering block accumulator loop for bucket 5:\nGetting block 8 of 60\n bucket 4: 40%\n bucket 5: 10%\n bucket 4: 50%\n bucket 2: 50%\n bucket 6: 30%\n bucket 1: 50%\n bucket 4: 60%\n bucket 6: 40%\n Reserving size (126) for bucket 8\n bucket 3: 30%\n bucket 2: 60%\n bucket 4: 70%\n bucket 1: 60%\n Calculating Z arrays for bucket 8\n bucket 3: 40%\n bucket 6: 50%\n bucket 4: 80%\n bucket 7: 20%\n bucket 6: 60%\n bucket 1: 70%\n bucket 5: 20%\n bucket 4: 90%\n bucket 1: 80%\n bucket 7: 30%\n bucket 6: 70%\n bucket 5: 30%\n bucket 4: 100%\n bucket 6: 80%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 2: 70%\n bucket 6: 90%\n bucket 1: 90%\n Entering block accumulator loop for bucket 8:\n bucket 2: 80%\n bucket 6: 100%\n bucket 5: 40%\n bucket 2: 90%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 3: 50%\n bucket 1: 100%\n bucket 5: 50%\n bucket 8: 10%\n Sorting block of length 42 for bucket 1\n bucket 7: 40%\n bucket 2: 100%\n (Using difference cover)\n bucket 5: 60%\n bucket 8: 20%\n bucket 3: 60%\n bucket 7: 50%\n Sorting block of length 84 for bucket 2\n bucket 7: 60%\n bucket 8: 30%\n bucket 3: 70%\n bucket 7: 70%\n (Using difference cover)\n bucket 8: 40%\n bucket 3: 80%\n bucket 7: 80%\n bucket 5: 70%\n bucket 8: 50%\n bucket 3: 90%\n bucket 7: 90%\n bucket 5: 80%\n bucket 7: 100%\n bucket 8: 60%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 90%\n bucket 8: 70%\n bucket 8: 80%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n bucket 8: 90%\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 3: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\nGetting block 9 of 60\n Reserving size (126) 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 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 10:\n bucket 11: 10%\n bucket 10: 10%\n Sorting block time: 00:00:00\n bucket 11: 20%\nReturning block of 125 for bucket 9\n bucket 10: 20%\n bucket 11: 30%\n bucket 10: 30%\n bucket 11: 40%\n bucket 10: 40%\n bucket 11: 50%\n bucket 10: 50%\n bucket 11: 60%\n bucket 10: 60%\n bucket 10: 70%\n bucket 11: 70%\n bucket 10: 80%\n bucket 11: 80%\n bucket 10: 90%\n bucket 11: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n Entering block accumulator loop for bucket 13:\n bucket 12: 30%\n bucket 13: 10%\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\n bucket 13: 40%\n bucket 12: 70%\n bucket 13: 50%\n bucket 12: 80%\n bucket 13: 60%\n bucket 12: 90%\n bucket 13: 70%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Entering block accumulator loop for bucket 14:\n Calculating Z arrays for bucket 15\n bucket 14: 10%\n Entering block accumulator loop for bucket 15:\n bucket 14: 20%\n bucket 15: 10%\n bucket 14: 30%\n bucket 15: 20%\n bucket 14: 40%\n bucket 15: 30%\n bucket 15: 40%\n bucket 14: 50%\n bucket 15: 50%\n bucket 14: 60%\n bucket 15: 60%\n bucket 14: 70%\n bucket 15: 70%\n bucket 14: 80%\n bucket 15: 80%\n bucket 15: 90%\n bucket 14: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n Entering block accumulator loop for bucket 17:\n bucket 16: 10%\n bucket 17: 10%\n bucket 17: 20%\n bucket 16: 20%\n bucket 17: 30%\n bucket 16: 30%\n bucket 17: 40%\n bucket 16: 40%\n bucket 17: 50%\n bucket 16: 50%\n bucket 17: 60%\n bucket 16: 60%\n bucket 17: 70%\n bucket 16: 70%\n bucket 17: 80%\n bucket 16: 80%\n bucket 16: 90%\n bucket 17: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) 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%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\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 122 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 bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) 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%\nGetting block 21 of 60\n bucket 20: 40%\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 50%\n bucket 20: 60%\n Entering block accumulator loop for bucket 21:\n bucket 20: 70%\n bucket 20: 80%\n bucket 21: 10%\n bucket 20: 90%\n bucket 21: 20%\n bucket 20: 100%\n bucket 21: 30%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\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 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) 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 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 30%\n bucket 22: 40%\n Entering block accumulator loop for bucket 23:\n bucket 22: 50%\n bucket 23: 10%\n bucket 22: 60%\n bucket 23: 20%\n bucket 22: 70%\n bucket 23: 30%\n bucket 22: 80%\n bucket 23: 40%\n bucket 22: 90%\n bucket 23: 50%\n bucket 22: 100%\n bucket 23: 60%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 24:\n bucket 25: 10%\n bucket 24: 10%\n bucket 25: 20%\n bucket 24: 20%\n bucket 25: 30%\n bucket 24: 30%\n bucket 25: 40%\n bucket 24: 40%\n bucket 25: 50%\n bucket 24: 50%\n bucket 25: 60%\n bucket 24: 60%\n bucket 25: 70%\n bucket 24: 70%\n bucket 25: 80%\n bucket 24: 80%\n bucket 25: 90%\n bucket 24: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Entering block accumulator loop for bucket 26:\n Reserving size (126) 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 26: 50%\n bucket 27: 30%\n bucket 26: 60%\n bucket 27: 40%\n bucket 26: 70%\n bucket 27: 50%\n bucket 26: 80%\n bucket 27: 60%\n bucket 26: 90%\n bucket 27: 70%\n bucket 26: 100%\n bucket 27: 80%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Entering block accumulator loop for bucket 28:\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 10%\n bucket 28: 20%\n Entering block accumulator loop for bucket 29:\n bucket 28: 30%\n bucket 29: 10%\n bucket 28: 40%\n bucket 29: 20%\n bucket 28: 50%\n bucket 29: 30%\n bucket 28: 60%\n bucket 29: 40%\n bucket 28: 70%\n bucket 29: 50%\n bucket 28: 80%\n bucket 29: 60%\n bucket 28: 90%\n bucket 29: 70%\n bucket 29: 80%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 60\n Entering block accumulator loop for bucket 30:\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 30: 10%\n bucket 30: 20%\n Entering block accumulator loop for bucket 31:\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 31: 10%\n bucket 30: 60%\n bucket 30: 70%\n bucket 31: 20%\n bucket 30: 80%\n bucket 30: 90%\n bucket 31: 30%\n bucket 30: 100%\n bucket 31: 40%\n Sorting block of length 124 for bucket 30\n bucket 31: 50%\n (Using difference cover)\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\n bucket 32: 40%\n bucket 32: 50%\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 33\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 33:\n bucket 34: 20%\n bucket 34: 30%\n bucket 33: 10%\n bucket 34: 40%\n bucket 34: 50%\n bucket 33: 20%\n bucket 34: 60%\n bucket 33: 30%\n bucket 34: 70%\n bucket 34: 80%\n bucket 33: 40%\n bucket 34: 90%\n bucket 33: 50%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Entering block accumulator loop for bucket 35:\n Calculating Z arrays for bucket 36\n bucket 35: 10%\n Entering block accumulator loop for bucket 36:\n bucket 35: 20%\n bucket 36: 10%\n bucket 35: 30%\n bucket 36: 20%\n bucket 35: 40%\n bucket 36: 30%\n bucket 35: 50%\n bucket 36: 40%\n bucket 35: 60%\n bucket 36: 50%\n bucket 35: 70%\n bucket 36: 60%\n bucket 35: 80%\n bucket 36: 70%\n bucket 35: 90%\n bucket 36: 80%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n bucket 36: 90%\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\nGetting block 39 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 39:\n bucket 38: 10%\n bucket 39: 10%\n bucket 38: 20%\n bucket 39: 20%\n bucket 38: 30%\n bucket 39: 30%\n bucket 38: 40%\n bucket 39: 40%\n bucket 38: 50%\n bucket 39: 50%\n bucket 38: 60%\n bucket 39: 60%\n bucket 38: 70%\n bucket 39: 70%\n bucket 38: 80%\n bucket 39: 80%\n bucket 38: 90%\n bucket 39: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n bucket 40: 20%\n Calculating Z arrays for bucket 41\n bucket 40: 30%\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 40: 40%\n bucket 41: 20%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 40: 60%\n bucket 41: 50%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 41: 90%\n bucket 40: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Entering block accumulator loop for bucket 43:\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n bucket 43: 10%\n bucket 43: 20%\n Entering block accumulator loop for bucket 44:\n bucket 43: 30%\n bucket 43: 40%\n bucket 44: 10%\n bucket 43: 50%\n bucket 44: 20%\n bucket 43: 60%\n bucket 44: 30%\n bucket 43: 70%\n bucket 44: 40%\n bucket 43: 80%\n bucket 44: 50%\n bucket 43: 90%\n bucket 44: 60%\n bucket 44: 70%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n Entering block accumulator loop for bucket 46:\n bucket 45: 30%\n bucket 45: 40%\n bucket 46: 10%\n bucket 45: 50%\n bucket 46: 20%\n bucket 45: 60%\n bucket 46: 30%\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 40%\n bucket 45: 90%\n bucket 46: 50%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n bucket 46: 60%\n (Using difference cover)\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\nGetting block 49 of 60\n bucket 48: 10%\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 48: 20%\n bucket 48: 30%\n Entering block accumulator loop for bucket 49:\n bucket 48: 40%\n bucket 49: 10%\n bucket 48: 50%\n bucket 48: 60%\n bucket 49: 20%\n bucket 48: 70%\n bucket 49: 30%\n bucket 48: 80%\n bucket 49: 40%\n bucket 48: 90%\n bucket 49: 50%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n bucket 50: 100%\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n Entering block accumulator loop for bucket 52:\n bucket 51: 40%\n bucket 51: 50%\n bucket 52: 10%\n bucket 51: 60%\n bucket 51: 70%\n bucket 52: 20%\n bucket 51: 80%\n bucket 51: 90%\n bucket 52: 30%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 40%\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n Sorting block time: 00:00:00\n bucket 52: 90%\nReturning block of 92 for bucket 51\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\nGetting block 55 of 60\n bucket 54: 30%\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 40%\n bucket 54: 50%\n Entering block accumulator loop for bucket 55:\n bucket 54: 60%\n bucket 54: 70%\n bucket 55: 10%\n bucket 54: 80%\n bucket 55: 20%\n bucket 54: 90%\n bucket 55: 30%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\nGetting block 57 of 60\n bucket 56: 50%\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n Entering block accumulator loop for bucket 57:\n bucket 56: 90%\n bucket 56: 100%\n bucket 57: 10%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n bucket 58: 90%\n Calculating Z arrays for bucket 59\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\nGetting block 3 of 60\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 3\nGetting block 4 of 60\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n Entering block accumulator loop for bucket 2:\n bucket 1: 10%\n Reserving size (126) for bucket 4\nGetting block 6 of 60\n Calculating Z arrays for bucket 3\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n Calculating Z arrays for bucket 4\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 7\n bucket 2: 10%\n Calculating Z arrays for bucket 6\n bucket 1: 20%\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 7:\n bucket 4: 10%\n Entering block accumulator loop for bucket 6:\n bucket 2: 20%\n Calculating Z arrays for bucket 5\n bucket 6: 10%\n Entering block accumulator loop for bucket 3:\n bucket 4: 20%\n bucket 1: 30%\n bucket 2: 30%\n bucket 6: 20%\n bucket 3: 10%\n bucket 2: 40%\n bucket 4: 30%\n bucket 1: 40%\n bucket 7: 10%\n bucket 3: 20%\n Entering block accumulator loop for bucket 5:\nGetting block 8 of 60\n bucket 4: 40%\n bucket 5: 10%\n bucket 4: 50%\n bucket 2: 50%\n bucket 6: 30%\n bucket 1: 50%\n bucket 4: 60%\n bucket 6: 40%\n Reserving size (126) for bucket 8\n bucket 3: 30%\n bucket 2: 60%\n bucket 4: 70%\n bucket 1: 60%\n Calculating Z arrays for bucket 8\n bucket 3: 40%\n bucket 6: 50%\n bucket 4: 80%\n bucket 7: 20%\n bucket 6: 60%\n bucket 1: 70%\n bucket 5: 20%\n bucket 4: 90%\n bucket 1: 80%\n bucket 7: 30%\n bucket 6: 70%\n bucket 5: 30%\n bucket 4: 100%\n bucket 6: 80%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 2: 70%\n bucket 6: 90%\n bucket 1: 90%\n Entering block accumulator loop for bucket 8:\n bucket 2: 80%\n bucket 6: 100%\n bucket 5: 40%\n bucket 2: 90%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 3: 50%\n bucket 1: 100%\n bucket 5: 50%\n bucket 8: 10%\n Sorting block of length 42 for bucket 1\n bucket 7: 40%\n bucket 2: 100%\n (Using difference cover)\n bucket 5: 60%\n bucket 8: 20%\n bucket 3: 60%\n bucket 7: 50%\n Sorting block of length 84 for bucket 2\n bucket 7: 60%\n bucket 8: 30%\n bucket 3: 70%\n bucket 7: 70%\n (Using difference cover)\n bucket 8: 40%\n bucket 3: 80%\n bucket 7: 80%\n bucket 5: 70%\n bucket 8: 50%\n bucket 3: 90%\n bucket 7: 90%\n bucket 5: 80%\n bucket 7: 100%\n bucket 8: 60%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 90%\n bucket 8: 70%\n bucket 8: 80%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n bucket 8: 90%\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 3: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\nGetting block 9 of 60\n Reserving size (126) 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 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 10:\n bucket 11: 10%\n bucket 10: 10%\n Sorting block time: 00:00:00\n bucket 11: 20%\nReturning block of 125 for bucket 9\n bucket 10: 20%\n bucket 11: 30%\n bucket 10: 30%\n bucket 11: 40%\n bucket 10: 40%\n bucket 11: 50%\n bucket 10: 50%\n bucket 11: 60%\n bucket 10: 60%\n bucket 10: 70%\n bucket 11: 70%\n bucket 10: 80%\n bucket 11: 80%\n bucket 10: 90%\n bucket 11: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n Entering block accumulator loop for bucket 13:\n bucket 12: 30%\n bucket 13: 10%\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\n bucket 13: 40%\n bucket 12: 70%\n bucket 13: 50%\n bucket 12: 80%\n bucket 13: 60%\n bucket 12: 90%\n bucket 13: 70%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Entering block accumulator loop for bucket 14:\n Calculating Z arrays for bucket 15\n bucket 14: 10%\n Entering block accumulator loop for bucket 15:\n bucket 14: 20%\n bucket 15: 10%\n bucket 14: 30%\n bucket 15: 20%\n bucket 14: 40%\n bucket 15: 30%\n bucket 15: 40%\n bucket 14: 50%\n bucket 15: 50%\n bucket 14: 60%\n bucket 15: 60%\n bucket 14: 70%\n bucket 15: 70%\n bucket 14: 80%\n bucket 15: 80%\n bucket 15: 90%\n bucket 14: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n Entering block accumulator loop for bucket 17:\n bucket 16: 10%\n bucket 17: 10%\n bucket 17: 20%\n bucket 16: 20%\n bucket 17: 30%\n bucket 16: 30%\n bucket 17: 40%\n bucket 16: 40%\n bucket 17: 50%\n bucket 16: 50%\n bucket 17: 60%\n bucket 16: 60%\n bucket 17: 70%\n bucket 16: 70%\n bucket 17: 80%\n bucket 16: 80%\n bucket 16: 90%\n bucket 17: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) 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%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\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 122 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 bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) 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%\nGetting block 21 of 60\n bucket 20: 40%\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 50%\n bucket 20: 60%\n Entering block accumulator loop for bucket 21:\n bucket 20: 70%\n bucket 20: 80%\n bucket 21: 10%\n bucket 20: 90%\n bucket 21: 20%\n bucket 20: 100%\n bucket 21: 30%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\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 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) 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 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 30%\n bucket 22: 40%\n Entering block accumulator loop for bucket 23:\n bucket 22: 50%\n bucket 23: 10%\n bucket 22: 60%\n bucket 23: 20%\n bucket 22: 70%\n bucket 23: 30%\n bucket 22: 80%\n bucket 23: 40%\n bucket 22: 90%\n bucket 23: 50%\n bucket 22: 100%\n bucket 23: 60%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 24:\n bucket 25: 10%\n bucket 24: 10%\n bucket 25: 20%\n bucket 24: 20%\n bucket 25: 30%\n bucket 24: 30%\n bucket 25: 40%\n bucket 24: 40%\n bucket 25: 50%\n bucket 24: 50%\n bucket 25: 60%\n bucket 24: 60%\n bucket 25: 70%\n bucket 24: 70%\n bucket 25: 80%\n bucket 24: 80%\n bucket 25: 90%\n bucket 24: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Entering block accumulator loop for bucket 26:\n Reserving size (126) 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 26: 50%\n bucket 27: 30%\n bucket 26: 60%\n bucket 27: 40%\n bucket 26: 70%\n bucket 27: 50%\n bucket 26: 80%\n bucket 27: 60%\n bucket 26: 90%\n bucket 27: 70%\n bucket 26: 100%\n bucket 27: 80%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Entering block accumulator loop for bucket 28:\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 10%\n bucket 28: 20%\n Entering block accumulator loop for bucket 29:\n bucket 28: 30%\n bucket 29: 10%\n bucket 28: 40%\n bucket 29: 20%\n bucket 28: 50%\n bucket 29: 30%\n bucket 28: 60%\n bucket 29: 40%\n bucket 28: 70%\n bucket 29: 50%\n bucket 28: 80%\n bucket 29: 60%\n bucket 28: 90%\n bucket 29: 70%\n bucket 29: 80%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 60\n Entering block accumulator loop for bucket 30:\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 30: 10%\n bucket 30: 20%\n Entering block accumulator loop for bucket 31:\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 31: 10%\n bucket 30: 60%\n bucket 30: 70%\n bucket 31: 20%\n bucket 30: 80%\n bucket 30: 90%\n bucket 31: 30%\n bucket 30: 100%\n bucket 31: 40%\n Sorting block of length 124 for bucket 30\n bucket 31: 50%\n (Using difference cover)\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\n bucket 32: 40%\n bucket 32: 50%\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 33\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 33:\n bucket 34: 20%\n bucket 34: 30%\n bucket 33: 10%\n bucket 34: 40%\n bucket 34: 50%\n bucket 33: 20%\n bucket 34: 60%\n bucket 33: 30%\n bucket 34: 70%\n bucket 34: 80%\n bucket 33: 40%\n bucket 34: 90%\n bucket 33: 50%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Entering block accumulator loop for bucket 35:\n Calculating Z arrays for bucket 36\n bucket 35: 10%\n Entering block accumulator loop for bucket 36:\n bucket 35: 20%\n bucket 36: 10%\n bucket 35: 30%\n bucket 36: 20%\n bucket 35: 40%\n bucket 36: 30%\n bucket 35: 50%\n bucket 36: 40%\n bucket 35: 60%\n bucket 36: 50%\n bucket 35: 70%\n bucket 36: 60%\n bucket 35: 80%\n bucket 36: 70%\n bucket 35: 90%\n bucket 36: 80%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n bucket 36: 90%\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\nGetting block 39 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 39:\n bucket 38: 10%\n bucket 39: 10%\n bucket 38: 20%\n bucket 39: 20%\n bucket 38: 30%\n bucket 39: 30%\n bucket 38: 40%\n bucket 39: 40%\n bucket 38: 50%\n bucket 39: 50%\n bucket 38: 60%\n bucket 39: 60%\n bucket 38: 70%\n bucket 39: 70%\n bucket 38: 80%\n bucket 39: 80%\n bucket 38: 90%\n bucket 39: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n bucket 40: 20%\n Calculating Z arrays for bucket 41\n bucket 40: 30%\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 40: 40%\n bucket 41: 20%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 40: 60%\n bucket 41: 50%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 41: 90%\n bucket 40: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Entering block accumulator loop for bucket 43:\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n bucket 43: 10%\n bucket 43: 20%\n Entering block accumulator loop for bucket 44:\n bucket 43: 30%\n bucket 43: 40%\n bucket 44: 10%\n bucket 43: 50%\n bucket 44: 20%\n bucket 43: 60%\n bucket 44: 30%\n bucket 43: 70%\n bucket 44: 40%\n bucket 43: 80%\n bucket 44: 50%\n bucket 43: 90%\n bucket 44: 60%\n bucket 44: 70%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n Entering block accumulator loop for bucket 46:\n bucket 45: 30%\n bucket 45: 40%\n bucket 46: 10%\n bucket 45: 50%\n bucket 46: 20%\n bucket 45: 60%\n bucket 46: 30%\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 40%\n bucket 45: 90%\n bucket 46: 50%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n bucket 46: 60%\n (Using difference cover)\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\nGetting block 49 of 60\n bucket 48: 10%\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 48: 20%\n bucket 48: 30%\n Entering block accumulator loop for bucket 49:\n bucket 48: 40%\n bucket 49: 10%\n bucket 48: 50%\n bucket 48: 60%\n bucket 49: 20%\n bucket 48: 70%\n bucket 49: 30%\n bucket 48: 80%\n bucket 49: 40%\n bucket 48: 90%\n bucket 49: 50%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n bucket 50: 100%\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n Entering block accumulator loop for bucket 52:\n bucket 51: 40%\n bucket 51: 50%\n bucket 52: 10%\n bucket 51: 60%\n bucket 51: 70%\n bucket 52: 20%\n bucket 51: 80%\n bucket 51: 90%\n bucket 52: 30%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 40%\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n Sorting block time: 00:00:00\n bucket 52: 90%\nReturning block of 92 for bucket 51\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\nGetting block 55 of 60\n bucket 54: 30%\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 40%\n bucket 54: 50%\n Entering block accumulator loop for bucket 55:\n bucket 54: 60%\n bucket 54: 70%\n bucket 55: 10%\n bucket 54: 80%\n bucket 55: 20%\n bucket 54: 90%\n bucket 55: 30%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\nGetting block 57 of 60\n bucket 56: 50%\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n Entering block accumulator loop for bucket 57:\n bucket 56: 90%\n bucket 56: 100%\n bucket 57: 10%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n bucket 58: 90%\n Calculating Z arrays for bucket 59\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:40:30", "plugin": "core", "name": "end_epoch", "raw_value": "1736862030.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:40:29", "plugin": "core", "name": "start_epoch", "raw_value": "1736862029.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 30.636262893676758, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "e254181fd93402c4"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "91153b3c900a0d21"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "03231a858175433d", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:41:09.922932", "create_time": "2025-01-14T13:40:58.403850", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-glvpt", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/4/1/6/dataset_416c24d3-13c6-4abd-b7f0-8910ebfeebf0.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/4/4/4/dataset_4443d662-06cb-40cc-98e2-078be3340928.dat' > input_f.fastq && seqtk seq -2 '/galaxy/server/database/objects/4/4/4/dataset_4443d662-06cb-40cc-98e2-078be3340928.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/8/d/a/dataset_8da4a35a-9b68-4ac3-8003-0cb69bcc0fb0.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\": 247, \"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\": 246, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "e254181fd93402c4", "src": "hda", "uuid": "416c24d3-13c6-4abd-b7f0-8910ebfeebf0"}, "library|input_1": {"id": "91153b3c900a0d21", "src": "hda", "uuid": "4443d662-06cb-40cc-98e2-078be3340928"}}, "outputs": {"output_alignments": {"id": "d1f316ac4919d5c1", "src": "hda", "uuid": "8da4a35a-9b68-4ac3-8003-0cb69bcc0fb0"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n bucket 1: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 2:\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n bucket 2: 10%\nGetting block 4 of 60\n Calculating Z arrays for bucket 3\n bucket 2: 20%\n Reserving size (126) for bucket 4\n bucket 1: 30%\n Calculating Z arrays for bucket 4\n bucket 2: 30%\n bucket 1: 40%\n Entering block accumulator loop for bucket 3:\nGetting block 5 of 60\n bucket 1: 50%\n Entering block accumulator loop for bucket 4:\n bucket 1: 60%\n bucket 2: 40%\n bucket 3: 10%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Reserving size (126) for bucket 5\n bucket 3: 20%\n bucket 4: 10%\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 6\nGetting block 7 of 60\n bucket 4: 20%\n bucket 1: 70%\n bucket 3: 30%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 5:\n bucket 1: 80%\n bucket 3: 40%\n bucket 4: 30%\n bucket 2: 50%\n bucket 1: 90%\n Entering block accumulator loop for bucket 6:\n bucket 5: 10%\n Calculating Z arrays for bucket 7\n bucket 1: 100%\n bucket 4: 40%\n bucket 3: 50%\n Sorting block of length 42 for bucket 1\n bucket 6: 10%\n (Using difference cover)\n bucket 5: 20%\n bucket 4: 50%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 6: 20%\n bucket 4: 60%\n bucket 5: 30%\n bucket 3: 60%\n bucket 4: 70%\n bucket 6: 30%\n bucket 5: 40%\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 7:\n bucket 6: 40%\n bucket 4: 80%\n bucket 5: 50%\n bucket 2: 60%\n bucket 7: 10%\n bucket 6: 50%\n bucket 4: 90%\n bucket 5: 60%\n bucket 3: 70%\n bucket 7: 20%\n bucket 4: 100%\n bucket 2: 70%\n bucket 6: 60%\n Entering block accumulator loop for bucket 8:\n bucket 5: 70%\n bucket 3: 80%\n bucket 2: 80%\n bucket 6: 70%\n bucket 2: 90%\n bucket 3: 90%\n Sorting block of length 68 for bucket 4\n bucket 3: 100%\n Sorting block time: 00:00:00\n bucket 8: 10%\nReturning block of 43 for bucket 1\n bucket 6: 80%\n bucket 2: 100%\n bucket 8: 20%\n bucket 5: 80%\n Sorting block of length 84 for bucket 2\n bucket 6: 90%\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n bucket 7: 30%\n (Using difference cover)\n (Using difference cover)\n bucket 6: 100%\n bucket 7: 40%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 30%\n bucket 7: 50%\n bucket 5: 90%\n bucket 7: 60%\n bucket 8: 40%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n bucket 7: 70%\n (Using difference cover)\n bucket 8: 50%\n bucket 7: 80%\n bucket 8: 60%\n bucket 7: 90%\n bucket 7: 100%\n bucket 8: 70%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) 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%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n bucket 9: 80%\n Calculating Z arrays for bucket 10\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 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 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) 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%\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 40%\n bucket 11: 50%\n Entering block accumulator loop for bucket 12:\n bucket 11: 60%\n bucket 12: 10%\n bucket 11: 70%\n bucket 12: 20%\n bucket 11: 80%\n bucket 12: 30%\n bucket 11: 90%\n bucket 12: 40%\n bucket 11: 100%\n bucket 12: 50%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\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 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 13 of 60\n Reserving size (126) 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%\nGetting block 14 of 60\n bucket 13: 30%\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n Entering block accumulator loop for bucket 14:\n bucket 13: 70%\n bucket 14: 10%\n bucket 13: 80%\n bucket 14: 20%\n bucket 13: 90%\n bucket 14: 30%\n bucket 13: 100%\n bucket 14: 40%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\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 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) 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 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 20%\n bucket 16: 30%\n Entering block accumulator loop for bucket 17:\n bucket 16: 40%\n bucket 17: 10%\n bucket 17: 20%\n bucket 16: 50%\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 30%\n bucket 16: 60%\n bucket 17: 40%\n bucket 16: 70%\n Entering block accumulator loop for bucket 18:\n bucket 17: 50%\n bucket 16: 80%\n bucket 18: 10%\n bucket 17: 60%\n bucket 16: 90%\n bucket 18: 20%\n bucket 17: 70%\n bucket 18: 30%\n bucket 17: 80%\n bucket 18: 40%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n bucket 18: 50%\n bucket 17: 90%\n bucket 18: 60%\n bucket 18: 70%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n bucket 18: 80%\n (Using difference cover)\n bucket 18: 90%\n (Using difference cover)\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n bucket 20: 50%\n bucket 19: 70%\n bucket 20: 60%\n bucket 19: 80%\n bucket 20: 70%\n bucket 19: 90%\n bucket 20: 80%\n bucket 19: 100%\n bucket 20: 90%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Entering block accumulator loop for bucket 21:\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 10%\n bucket 21: 20%\n Entering block accumulator loop for bucket 22:\n bucket 21: 30%\n bucket 21: 40%\n bucket 22: 10%\n bucket 21: 50%\n bucket 22: 20%\n bucket 21: 60%\n bucket 22: 30%\n bucket 21: 70%\n bucket 22: 40%\n bucket 21: 80%\n bucket 22: 50%\n bucket 21: 90%\n bucket 22: 60%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\nGetting block 24 of 60\n Calculating Z arrays for bucket 23\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n Entering block accumulator loop for bucket 24:\n bucket 23: 10%\n bucket 24: 10%\n bucket 23: 20%\n bucket 23: 30%\nGetting block 25 of 60\n bucket 24: 20%\n Reserving size (126) for bucket 25\n bucket 23: 40%\n bucket 24: 30%\n Calculating Z arrays for bucket 25\n bucket 23: 50%\n bucket 24: 40%\n Entering block accumulator loop for bucket 25:\n bucket 24: 50%\n bucket 23: 60%\n bucket 24: 60%\n bucket 25: 10%\n bucket 23: 70%\n bucket 24: 70%\n bucket 25: 20%\n bucket 23: 80%\n bucket 24: 80%\n bucket 25: 30%\n bucket 23: 90%\n bucket 24: 90%\n bucket 25: 40%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 25: 50%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n bucket 25: 60%\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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Reserving size (126) for bucket 27\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 27: 50%\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 119 for bucket 27\n bucket 28: 90%\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 30:\n bucket 29: 10%\n bucket 30: 10%\n bucket 29: 20%\n bucket 30: 20%\n bucket 29: 30%\n bucket 30: 30%\n bucket 29: 40%\n bucket 30: 40%\n bucket 29: 50%\n bucket 30: 50%\n bucket 29: 60%\n bucket 30: 60%\n bucket 29: 70%\n bucket 30: 70%\n bucket 29: 80%\n bucket 30: 80%\n bucket 29: 90%\n bucket 30: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 32: 10%\n bucket 31: 30%\n bucket 32: 20%\n bucket 31: 40%\n bucket 32: 30%\n bucket 31: 50%\n bucket 32: 40%\n bucket 31: 60%\n bucket 32: 50%\n bucket 31: 70%\n bucket 32: 60%\n bucket 31: 80%\n bucket 32: 70%\n bucket 31: 90%\n bucket 32: 80%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 60%\n bucket 35: 70%\n Entering block accumulator loop for bucket 36:\n bucket 35: 80%\n bucket 36: 10%\n bucket 35: 90%\n bucket 36: 20%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 37:\n Entering block accumulator loop for bucket 38:\n bucket 37: 10%\n bucket 38: 10%\n bucket 37: 20%\n bucket 38: 20%\n bucket 38: 30%\n bucket 37: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 37: 40%\n bucket 38: 60%\n bucket 38: 70%\n bucket 37: 50%\n bucket 38: 80%\n bucket 38: 90%\n bucket 37: 60%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 39 of 60\n Reserving size (126) for bucket 39\nGetting block 40 of 60\n Calculating Z arrays for bucket 39\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 40: 20%\n bucket 39: 30%\n bucket 40: 30%\n bucket 39: 40%\n bucket 40: 40%\n bucket 39: 50%\n bucket 40: 50%\n bucket 39: 60%\n bucket 40: 60%\n bucket 39: 70%\n bucket 40: 70%\n bucket 39: 80%\n bucket 40: 80%\n bucket 39: 90%\n bucket 40: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 43:\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n bucket 42: 10%\n Calculating Z arrays for bucket 44\n bucket 43: 10%\n bucket 42: 20%\n bucket 43: 20%\n Entering block accumulator loop for bucket 44:\n bucket 43: 30%\n bucket 42: 30%\n bucket 44: 10%\n bucket 43: 40%\n bucket 44: 20%\n bucket 42: 40%\n bucket 43: 50%\n bucket 44: 30%\n bucket 44: 40%\n bucket 43: 60%\n bucket 42: 50%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 42: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 44: 80%\n bucket 43: 90%\n bucket 42: 70%\n bucket 44: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\nGetting block 46 of 60\n bucket 45: 30%\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n Entering block accumulator loop for bucket 46:\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 10%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\nGetting block 48 of 60\n bucket 47: 10%\n Reserving size (126) for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 47: 20%\n Calculating Z arrays for bucket 48\n bucket 47: 30%\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 48:\n bucket 47: 40%\n bucket 47: 50%\n bucket 48: 10%\n bucket 49: 10%\n bucket 47: 60%\n bucket 48: 20%\n bucket 49: 20%\n bucket 47: 70%\n bucket 48: 30%\n bucket 47: 80%\n bucket 49: 30%\n bucket 47: 90%\n bucket 48: 40%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 49: 40%\n bucket 48: 50%\n bucket 49: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 49: 60%\n bucket 48: 80%\n bucket 49: 70%\n bucket 48: 90%\n bucket 49: 80%\n bucket 48: 100%\n bucket 49: 90%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n bucket 51: 20%\n Entering block accumulator loop for bucket 52:\n bucket 51: 30%\n bucket 52: 10%\n bucket 51: 40%\n bucket 52: 20%\n bucket 51: 50%\n bucket 52: 30%\n bucket 51: 60%\n bucket 52: 40%\n bucket 51: 70%\n bucket 52: 50%\n bucket 51: 80%\n bucket 52: 60%\n bucket 51: 90%\n bucket 52: 70%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\nGetting block 54 of 60\n bucket 53: 10%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 20%\n bucket 53: 30%\n Entering block accumulator loop for bucket 54:\n bucket 53: 40%\n bucket 54: 10%\n bucket 53: 50%\n bucket 54: 20%\n bucket 53: 60%\n bucket 54: 30%\n bucket 53: 70%\n bucket 54: 40%\n bucket 53: 80%\n bucket 53: 90%\n bucket 54: 50%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Entering block accumulator loop for bucket 55:\n Calculating Z arrays for bucket 56\n bucket 55: 10%\n bucket 55: 20%\n Entering block accumulator loop for bucket 56:\n bucket 55: 30%\n bucket 56: 10%\n bucket 55: 40%\n bucket 56: 20%\n bucket 55: 50%\n bucket 56: 30%\n bucket 55: 60%\n bucket 55: 70%\n bucket 56: 40%\n bucket 55: 80%\n bucket 56: 50%\n bucket 55: 90%\n bucket 56: 60%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\nGetting block 58 of 60\n bucket 57: 30%\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 40%\n bucket 57: 50%\n Entering block accumulator loop for bucket 58:\n bucket 57: 60%\n bucket 57: 70%\n bucket 58: 10%\n bucket 57: 80%\n bucket 57: 90%\n bucket 58: 20%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\nGetting block 60 of 60\n bucket 59: 70%\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 80%\n bucket 59: 90%\n Entering block accumulator loop for bucket 60:\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n bucket 1: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 2:\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n bucket 2: 10%\nGetting block 4 of 60\n Calculating Z arrays for bucket 3\n bucket 2: 20%\n Reserving size (126) for bucket 4\n bucket 1: 30%\n Calculating Z arrays for bucket 4\n bucket 2: 30%\n bucket 1: 40%\n Entering block accumulator loop for bucket 3:\nGetting block 5 of 60\n bucket 1: 50%\n Entering block accumulator loop for bucket 4:\n bucket 1: 60%\n bucket 2: 40%\n bucket 3: 10%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Reserving size (126) for bucket 5\n bucket 3: 20%\n bucket 4: 10%\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 6\nGetting block 7 of 60\n bucket 4: 20%\n bucket 1: 70%\n bucket 3: 30%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 5:\n bucket 1: 80%\n bucket 3: 40%\n bucket 4: 30%\n bucket 2: 50%\n bucket 1: 90%\n Entering block accumulator loop for bucket 6:\n bucket 5: 10%\n Calculating Z arrays for bucket 7\n bucket 1: 100%\n bucket 4: 40%\n bucket 3: 50%\n Sorting block of length 42 for bucket 1\n bucket 6: 10%\n (Using difference cover)\n bucket 5: 20%\n bucket 4: 50%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 6: 20%\n bucket 4: 60%\n bucket 5: 30%\n bucket 3: 60%\n bucket 4: 70%\n bucket 6: 30%\n bucket 5: 40%\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 7:\n bucket 6: 40%\n bucket 4: 80%\n bucket 5: 50%\n bucket 2: 60%\n bucket 7: 10%\n bucket 6: 50%\n bucket 4: 90%\n bucket 5: 60%\n bucket 3: 70%\n bucket 7: 20%\n bucket 4: 100%\n bucket 2: 70%\n bucket 6: 60%\n Entering block accumulator loop for bucket 8:\n bucket 5: 70%\n bucket 3: 80%\n bucket 2: 80%\n bucket 6: 70%\n bucket 2: 90%\n bucket 3: 90%\n Sorting block of length 68 for bucket 4\n bucket 3: 100%\n Sorting block time: 00:00:00\n bucket 8: 10%\nReturning block of 43 for bucket 1\n bucket 6: 80%\n bucket 2: 100%\n bucket 8: 20%\n bucket 5: 80%\n Sorting block of length 84 for bucket 2\n bucket 6: 90%\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n bucket 7: 30%\n (Using difference cover)\n (Using difference cover)\n bucket 6: 100%\n bucket 7: 40%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 30%\n bucket 7: 50%\n bucket 5: 90%\n bucket 7: 60%\n bucket 8: 40%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n bucket 7: 70%\n (Using difference cover)\n bucket 8: 50%\n bucket 7: 80%\n bucket 8: 60%\n bucket 7: 90%\n bucket 7: 100%\n bucket 8: 70%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) 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%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n bucket 9: 80%\n Calculating Z arrays for bucket 10\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 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 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) 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%\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 40%\n bucket 11: 50%\n Entering block accumulator loop for bucket 12:\n bucket 11: 60%\n bucket 12: 10%\n bucket 11: 70%\n bucket 12: 20%\n bucket 11: 80%\n bucket 12: 30%\n bucket 11: 90%\n bucket 12: 40%\n bucket 11: 100%\n bucket 12: 50%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\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 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 13 of 60\n Reserving size (126) 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%\nGetting block 14 of 60\n bucket 13: 30%\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n Entering block accumulator loop for bucket 14:\n bucket 13: 70%\n bucket 14: 10%\n bucket 13: 80%\n bucket 14: 20%\n bucket 13: 90%\n bucket 14: 30%\n bucket 13: 100%\n bucket 14: 40%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\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 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) 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 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 20%\n bucket 16: 30%\n Entering block accumulator loop for bucket 17:\n bucket 16: 40%\n bucket 17: 10%\n bucket 17: 20%\n bucket 16: 50%\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 30%\n bucket 16: 60%\n bucket 17: 40%\n bucket 16: 70%\n Entering block accumulator loop for bucket 18:\n bucket 17: 50%\n bucket 16: 80%\n bucket 18: 10%\n bucket 17: 60%\n bucket 16: 90%\n bucket 18: 20%\n bucket 17: 70%\n bucket 18: 30%\n bucket 17: 80%\n bucket 18: 40%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n bucket 18: 50%\n bucket 17: 90%\n bucket 18: 60%\n bucket 18: 70%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n bucket 18: 80%\n (Using difference cover)\n bucket 18: 90%\n (Using difference cover)\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n bucket 20: 50%\n bucket 19: 70%\n bucket 20: 60%\n bucket 19: 80%\n bucket 20: 70%\n bucket 19: 90%\n bucket 20: 80%\n bucket 19: 100%\n bucket 20: 90%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Entering block accumulator loop for bucket 21:\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 10%\n bucket 21: 20%\n Entering block accumulator loop for bucket 22:\n bucket 21: 30%\n bucket 21: 40%\n bucket 22: 10%\n bucket 21: 50%\n bucket 22: 20%\n bucket 21: 60%\n bucket 22: 30%\n bucket 21: 70%\n bucket 22: 40%\n bucket 21: 80%\n bucket 22: 50%\n bucket 21: 90%\n bucket 22: 60%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\nGetting block 24 of 60\n Calculating Z arrays for bucket 23\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n Entering block accumulator loop for bucket 24:\n bucket 23: 10%\n bucket 24: 10%\n bucket 23: 20%\n bucket 23: 30%\nGetting block 25 of 60\n bucket 24: 20%\n Reserving size (126) for bucket 25\n bucket 23: 40%\n bucket 24: 30%\n Calculating Z arrays for bucket 25\n bucket 23: 50%\n bucket 24: 40%\n Entering block accumulator loop for bucket 25:\n bucket 24: 50%\n bucket 23: 60%\n bucket 24: 60%\n bucket 25: 10%\n bucket 23: 70%\n bucket 24: 70%\n bucket 25: 20%\n bucket 23: 80%\n bucket 24: 80%\n bucket 25: 30%\n bucket 23: 90%\n bucket 24: 90%\n bucket 25: 40%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 25: 50%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n bucket 25: 60%\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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Reserving size (126) for bucket 27\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 27: 50%\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 119 for bucket 27\n bucket 28: 90%\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 30:\n bucket 29: 10%\n bucket 30: 10%\n bucket 29: 20%\n bucket 30: 20%\n bucket 29: 30%\n bucket 30: 30%\n bucket 29: 40%\n bucket 30: 40%\n bucket 29: 50%\n bucket 30: 50%\n bucket 29: 60%\n bucket 30: 60%\n bucket 29: 70%\n bucket 30: 70%\n bucket 29: 80%\n bucket 30: 80%\n bucket 29: 90%\n bucket 30: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 32: 10%\n bucket 31: 30%\n bucket 32: 20%\n bucket 31: 40%\n bucket 32: 30%\n bucket 31: 50%\n bucket 32: 40%\n bucket 31: 60%\n bucket 32: 50%\n bucket 31: 70%\n bucket 32: 60%\n bucket 31: 80%\n bucket 32: 70%\n bucket 31: 90%\n bucket 32: 80%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 60%\n bucket 35: 70%\n Entering block accumulator loop for bucket 36:\n bucket 35: 80%\n bucket 36: 10%\n bucket 35: 90%\n bucket 36: 20%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 37:\n Entering block accumulator loop for bucket 38:\n bucket 37: 10%\n bucket 38: 10%\n bucket 37: 20%\n bucket 38: 20%\n bucket 38: 30%\n bucket 37: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 37: 40%\n bucket 38: 60%\n bucket 38: 70%\n bucket 37: 50%\n bucket 38: 80%\n bucket 38: 90%\n bucket 37: 60%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 39 of 60\n Reserving size (126) for bucket 39\nGetting block 40 of 60\n Calculating Z arrays for bucket 39\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 40: 20%\n bucket 39: 30%\n bucket 40: 30%\n bucket 39: 40%\n bucket 40: 40%\n bucket 39: 50%\n bucket 40: 50%\n bucket 39: 60%\n bucket 40: 60%\n bucket 39: 70%\n bucket 40: 70%\n bucket 39: 80%\n bucket 40: 80%\n bucket 39: 90%\n bucket 40: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 43:\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n bucket 42: 10%\n Calculating Z arrays for bucket 44\n bucket 43: 10%\n bucket 42: 20%\n bucket 43: 20%\n Entering block accumulator loop for bucket 44:\n bucket 43: 30%\n bucket 42: 30%\n bucket 44: 10%\n bucket 43: 40%\n bucket 44: 20%\n bucket 42: 40%\n bucket 43: 50%\n bucket 44: 30%\n bucket 44: 40%\n bucket 43: 60%\n bucket 42: 50%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 42: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 44: 80%\n bucket 43: 90%\n bucket 42: 70%\n bucket 44: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\nGetting block 46 of 60\n bucket 45: 30%\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n Entering block accumulator loop for bucket 46:\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 10%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\nGetting block 48 of 60\n bucket 47: 10%\n Reserving size (126) for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 47: 20%\n Calculating Z arrays for bucket 48\n bucket 47: 30%\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 48:\n bucket 47: 40%\n bucket 47: 50%\n bucket 48: 10%\n bucket 49: 10%\n bucket 47: 60%\n bucket 48: 20%\n bucket 49: 20%\n bucket 47: 70%\n bucket 48: 30%\n bucket 47: 80%\n bucket 49: 30%\n bucket 47: 90%\n bucket 48: 40%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 49: 40%\n bucket 48: 50%\n bucket 49: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 49: 60%\n bucket 48: 80%\n bucket 49: 70%\n bucket 48: 90%\n bucket 49: 80%\n bucket 48: 100%\n bucket 49: 90%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n bucket 51: 20%\n Entering block accumulator loop for bucket 52:\n bucket 51: 30%\n bucket 52: 10%\n bucket 51: 40%\n bucket 52: 20%\n bucket 51: 50%\n bucket 52: 30%\n bucket 51: 60%\n bucket 52: 40%\n bucket 51: 70%\n bucket 52: 50%\n bucket 51: 80%\n bucket 52: 60%\n bucket 51: 90%\n bucket 52: 70%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\nGetting block 54 of 60\n bucket 53: 10%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 20%\n bucket 53: 30%\n Entering block accumulator loop for bucket 54:\n bucket 53: 40%\n bucket 54: 10%\n bucket 53: 50%\n bucket 54: 20%\n bucket 53: 60%\n bucket 54: 30%\n bucket 53: 70%\n bucket 54: 40%\n bucket 53: 80%\n bucket 53: 90%\n bucket 54: 50%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Entering block accumulator loop for bucket 55:\n Calculating Z arrays for bucket 56\n bucket 55: 10%\n bucket 55: 20%\n Entering block accumulator loop for bucket 56:\n bucket 55: 30%\n bucket 56: 10%\n bucket 55: 40%\n bucket 56: 20%\n bucket 55: 50%\n bucket 56: 30%\n bucket 55: 60%\n bucket 55: 70%\n bucket 56: 40%\n bucket 55: 80%\n bucket 56: 50%\n bucket 55: 90%\n bucket 56: 60%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\nGetting block 58 of 60\n bucket 57: 30%\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 40%\n bucket 57: 50%\n Entering block accumulator loop for bucket 58:\n bucket 57: 60%\n bucket 57: 70%\n bucket 58: 10%\n bucket 57: 80%\n bucket 57: 90%\n bucket 58: 20%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\nGetting block 60 of 60\n bucket 59: 70%\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 80%\n bucket 59: 90%\n Entering block accumulator loop for bucket 60:\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:41:00", "plugin": "core", "name": "end_epoch", "raw_value": "1736862060.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:40:59", "plugin": "core", "name": "start_epoch", "raw_value": "1736862059.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 31.43423080444336, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "cb3d2473663a2c56"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "247e66e0738209a8"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "ab8c61ce197d5a3d", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:41:41.530884", "create_time": "2025-01-14T13:41:29.144721", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-kfqkj", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/5/5/6/dataset_5567fdf3-edee-400e-9a22-335aa51d65de.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/3/b/d/dataset_3bd3ca45-2c59-456d-92c2-e5ace80d155d.dat' > input_f.fasta && seqtk seq -2 '/galaxy/server/database/objects/3/b/d/dataset_3bd3ca45-2c59-456d-92c2-e5ace80d155d.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/6/b/b/dataset_6bba1edc-ef06-421d-8e04-5bfd4e178521.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\": 250, \"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\": 249, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "cb3d2473663a2c56", "src": "hda", "uuid": "5567fdf3-edee-400e-9a22-335aa51d65de"}, "library|input_1": {"id": "247e66e0738209a8", "src": "hda", "uuid": "3bd3ca45-2c59-456d-92c2-e5ace80d155d"}}, "outputs": {"output_alignments": {"id": "f16e8e8ad5e6c35e", "src": "hda", "uuid": "6bba1edc-ef06-421d-8e04-5bfd4e178521"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n bucket 1: 20%\nGetting block 3 of 60\n bucket 1: 30%\n Reserving size (126) for bucket 3\n bucket 1: 40%\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 50%\nGetting block 4 of 60\n Entering block accumulator loop for bucket 3:\n bucket 1: 60%\n bucket 2: 10%\n bucket 1: 70%\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 4\n bucket 1: 80%\n Calculating Z arrays for bucket 5\n bucket 3: 10%\n bucket 2: 20%\n bucket 1: 90%\n Entering block accumulator loop for bucket 4:\n bucket 1: 100%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Entering block accumulator loop for bucket 5:\n bucket 2: 30%\n bucket 3: 20%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 4: 10%\n bucket 5: 10%\n bucket 3: 30%\n bucket 4: 20%\n Calculating Z arrays for bucket 6\n bucket 5: 20%\nGetting block 7 of 60\n bucket 4: 30%\n bucket 3: 40%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 6:\n bucket 3: 50%\n bucket 2: 40%\n bucket 5: 30%\n bucket 3: 60%\n bucket 6: 10%\n bucket 5: 40%\n bucket 4: 40%\n bucket 3: 70%\n bucket 6: 20%\n Calculating Z arrays for bucket 7\n bucket 3: 80%\n Sorting block time: 00:00:00\nGetting block 8 of 60\n Reserving size (126) for bucket 8\nReturning block of 43 for bucket 1\n bucket 6: 30%\n bucket 2: 50%\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 7:\n bucket 2: 60%\n bucket 4: 50%\n bucket 5: 50%\n bucket 7: 10%\n bucket 3: 90%\n bucket 5: 60%\n bucket 2: 70%\n Entering block accumulator loop for bucket 8:\n bucket 4: 60%\n bucket 7: 20%\n bucket 3: 100%\n Sorting block of length 106 for bucket 3\n bucket 8: 10%\n bucket 7: 30%\n bucket 6: 40%\n bucket 2: 80%\n bucket 5: 70%\n bucket 8: 20%\n bucket 4: 70%\n bucket 5: 80%\n bucket 7: 40%\n (Using difference cover)\n bucket 6: 50%\n bucket 4: 80%\n bucket 8: 30%\n bucket 6: 60%\n bucket 5: 90%\n bucket 8: 40%\n bucket 4: 90%\n bucket 7: 50%\n bucket 8: 50%\n bucket 2: 90%\n bucket 7: 60%\n bucket 8: 60%\n bucket 6: 70%\n bucket 4: 100%\n bucket 2: 100%\n bucket 5: 100%\n bucket 8: 70%\n bucket 7: 70%\n Sorting block of length 68 for bucket 4\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 80%\n bucket 8: 80%\n Sorting block of length 84 for bucket 2\n bucket 6: 80%\n bucket 7: 90%\n bucket 8: 90%\n (Using difference cover)\n bucket 6: 90%\n (Using difference cover)\n bucket 7: 100%\n bucket 8: 100%\n bucket 6: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) 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 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 124 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\nGetting block 12 of 60\n bucket 11: 10%\n Reserving size (126) for bucket 12\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 Calculating Z arrays for bucket 12\n bucket 11: 80%\n bucket 11: 90%\n Entering block accumulator loop for bucket 12:\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\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 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n Entering block accumulator loop for bucket 14:\n bucket 13: 20%\n bucket 14: 10%\n bucket 13: 30%\n bucket 14: 20%\n bucket 13: 40%\n bucket 14: 30%\n bucket 14: 40%\n bucket 13: 50%\n bucket 14: 50%\n bucket 13: 60%\n bucket 14: 60%\n bucket 13: 70%\n bucket 14: 70%\n bucket 13: 80%\n bucket 14: 80%\n bucket 13: 90%\n bucket 14: 90%\n bucket 13: 100%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n bucket 15: 20%\n Calculating Z arrays for bucket 16\n bucket 15: 30%\n bucket 15: 40%\n Entering block accumulator loop for bucket 16:\n bucket 15: 50%\n bucket 15: 60%\n bucket 16: 10%\n bucket 15: 70%\n bucket 16: 20%\n bucket 15: 80%\n bucket 16: 30%\n bucket 15: 90%\n bucket 16: 40%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\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 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) 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%\nGetting block 18 of 60\n bucket 17: 80%\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 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 bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) 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 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) 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 97 for bucket 20\n (Using difference cover)\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\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 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 23: 20%\n bucket 22: 30%\n bucket 23: 30%\n bucket 22: 40%\n bucket 23: 40%\n bucket 22: 50%\n bucket 23: 50%\n bucket 22: 60%\n bucket 23: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 23: 70%\n bucket 22: 90%\n bucket 23: 80%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) 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 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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 25: 20%\n bucket 26: 10%\n bucket 25: 30%\n bucket 25: 40%\n bucket 26: 20%\n bucket 25: 50%\n bucket 25: 60%\n bucket 26: 30%\n bucket 25: 70%\n bucket 25: 80%\n bucket 26: 40%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\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 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) 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%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n bucket 27: 90%\n Calculating Z arrays for bucket 28\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\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 Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\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 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 30:\n bucket 29: 10%\n bucket 30: 10%\n bucket 29: 20%\n bucket 30: 20%\n bucket 29: 30%\n bucket 30: 30%\n bucket 29: 40%\n bucket 30: 40%\n bucket 29: 50%\n bucket 30: 50%\n bucket 29: 60%\n bucket 30: 60%\n bucket 29: 70%\n bucket 30: 70%\n bucket 29: 80%\n bucket 30: 80%\n bucket 29: 90%\n bucket 30: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 31: 30%\n bucket 32: 10%\n bucket 31: 40%\n bucket 31: 50%\n bucket 32: 20%\n bucket 31: 60%\n bucket 31: 70%\n bucket 32: 30%\n bucket 31: 80%\n bucket 32: 40%\n bucket 31: 90%\n bucket 32: 50%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Entering block accumulator loop for bucket 37:\n bucket 36: 70%\n Reserving size (126) for bucket 38\n bucket 37: 10%\n Calculating Z arrays for bucket 38\n bucket 36: 80%\n bucket 37: 20%\n bucket 37: 30%\n Entering block accumulator loop for bucket 38:\n bucket 36: 90%\n bucket 37: 40%\n bucket 38: 10%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n bucket 38: 20%\n (Using difference cover)\n bucket 37: 50%\n bucket 38: 30%\n bucket 37: 60%\n bucket 38: 40%\n bucket 37: 70%\n bucket 38: 50%\n bucket 37: 80%\n bucket 38: 60%\n bucket 37: 90%\n bucket 38: 70%\n bucket 37: 100%\n bucket 38: 80%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 90%\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\nGetting block 40 of 60\n Calculating Z arrays for bucket 39\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 39: 30%\n bucket 40: 20%\n bucket 39: 40%\n bucket 40: 30%\n bucket 39: 50%\n bucket 40: 40%\n bucket 39: 60%\n bucket 40: 50%\n bucket 39: 70%\n bucket 39: 80%\n bucket 40: 60%\n bucket 39: 90%\n bucket 40: 70%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 40%\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n bucket 42: 50%\n Entering block accumulator loop for bucket 43:\n bucket 42: 60%\n Entering block accumulator loop for bucket 44:\n bucket 43: 10%\n bucket 42: 70%\n bucket 44: 10%\n bucket 43: 20%\n bucket 42: 80%\n bucket 44: 20%\n bucket 43: 30%\n bucket 44: 30%\n bucket 43: 40%\n bucket 42: 90%\n bucket 44: 40%\n bucket 43: 50%\n bucket 42: 100%\n bucket 43: 60%\n Sorting block of length 119 for bucket 42\n bucket 44: 50%\n (Using difference cover)\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 43: 90%\n bucket 44: 80%\n bucket 43: 100%\n bucket 44: 90%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\nGetting block 46 of 60\n Reserving size (126) for bucket 45\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 45\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 46:\n bucket 45: 10%\n bucket 45: 20%\n bucket 46: 10%\n bucket 45: 30%\n bucket 46: 20%\n bucket 45: 40%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 40%\n bucket 45: 90%\n bucket 45: 100%\n bucket 46: 50%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n Entering block accumulator loop for bucket 48:\n bucket 47: 20%\n bucket 48: 10%\n bucket 47: 30%\n bucket 48: 20%\n bucket 47: 40%\n bucket 48: 30%\n bucket 47: 50%\n bucket 48: 40%\n bucket 47: 60%\n bucket 48: 50%\n bucket 47: 70%\n bucket 48: 60%\n bucket 47: 80%\n bucket 48: 70%\n bucket 47: 90%\n bucket 48: 80%\n bucket 47: 100%\n bucket 48: 90%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n bucket 50: 20%\n Calculating Z arrays for bucket 51\n bucket 50: 30%\n Entering block accumulator loop for bucket 51:\n bucket 50: 40%\n bucket 51: 10%\nGetting block 52 of 60\n bucket 51: 20%\n bucket 50: 50%\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 50: 60%\n bucket 51: 30%\n bucket 50: 70%\n bucket 51: 40%\n Entering block accumulator loop for bucket 52:\n bucket 50: 80%\n bucket 51: 50%\n bucket 52: 10%\n bucket 50: 90%\n bucket 51: 60%\n bucket 52: 20%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 70%\n bucket 52: 30%\n bucket 51: 80%\n bucket 52: 40%\n bucket 51: 90%\n bucket 52: 50%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n Entering block accumulator loop for bucket 54:\n bucket 53: 20%\n bucket 54: 10%\n bucket 54: 20%\n bucket 53: 30%\n bucket 54: 30%\n bucket 53: 40%\n bucket 54: 40%\n bucket 54: 50%\n bucket 53: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 53: 60%\n bucket 54: 80%\n bucket 54: 90%\n bucket 53: 70%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n Entering block accumulator loop for bucket 58:\n bucket 57: 10%\n bucket 58: 10%\n bucket 58: 20%\n bucket 57: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 57: 30%\n bucket 58: 50%\n bucket 57: 40%\n bucket 58: 60%\n bucket 58: 70%\n bucket 57: 50%\n bucket 58: 80%\n bucket 57: 60%\n bucket 58: 90%\n bucket 57: 70%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 59: 20%\n bucket 60: 20%\n bucket 60: 30%\n bucket 59: 30%\n bucket 60: 40%\n bucket 59: 40%\n bucket 60: 50%\n bucket 59: 50%\n bucket 60: 60%\n bucket 59: 60%\n bucket 60: 70%\n bucket 59: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n bucket 1: 20%\nGetting block 3 of 60\n bucket 1: 30%\n Reserving size (126) for bucket 3\n bucket 1: 40%\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 50%\nGetting block 4 of 60\n Entering block accumulator loop for bucket 3:\n bucket 1: 60%\n bucket 2: 10%\n bucket 1: 70%\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 4\n bucket 1: 80%\n Calculating Z arrays for bucket 5\n bucket 3: 10%\n bucket 2: 20%\n bucket 1: 90%\n Entering block accumulator loop for bucket 4:\n bucket 1: 100%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Entering block accumulator loop for bucket 5:\n bucket 2: 30%\n bucket 3: 20%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 4: 10%\n bucket 5: 10%\n bucket 3: 30%\n bucket 4: 20%\n Calculating Z arrays for bucket 6\n bucket 5: 20%\nGetting block 7 of 60\n bucket 4: 30%\n bucket 3: 40%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 6:\n bucket 3: 50%\n bucket 2: 40%\n bucket 5: 30%\n bucket 3: 60%\n bucket 6: 10%\n bucket 5: 40%\n bucket 4: 40%\n bucket 3: 70%\n bucket 6: 20%\n Calculating Z arrays for bucket 7\n bucket 3: 80%\n Sorting block time: 00:00:00\nGetting block 8 of 60\n Reserving size (126) for bucket 8\nReturning block of 43 for bucket 1\n bucket 6: 30%\n bucket 2: 50%\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 7:\n bucket 2: 60%\n bucket 4: 50%\n bucket 5: 50%\n bucket 7: 10%\n bucket 3: 90%\n bucket 5: 60%\n bucket 2: 70%\n Entering block accumulator loop for bucket 8:\n bucket 4: 60%\n bucket 7: 20%\n bucket 3: 100%\n Sorting block of length 106 for bucket 3\n bucket 8: 10%\n bucket 7: 30%\n bucket 6: 40%\n bucket 2: 80%\n bucket 5: 70%\n bucket 8: 20%\n bucket 4: 70%\n bucket 5: 80%\n bucket 7: 40%\n (Using difference cover)\n bucket 6: 50%\n bucket 4: 80%\n bucket 8: 30%\n bucket 6: 60%\n bucket 5: 90%\n bucket 8: 40%\n bucket 4: 90%\n bucket 7: 50%\n bucket 8: 50%\n bucket 2: 90%\n bucket 7: 60%\n bucket 8: 60%\n bucket 6: 70%\n bucket 4: 100%\n bucket 2: 100%\n bucket 5: 100%\n bucket 8: 70%\n bucket 7: 70%\n Sorting block of length 68 for bucket 4\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 80%\n bucket 8: 80%\n Sorting block of length 84 for bucket 2\n bucket 6: 80%\n bucket 7: 90%\n bucket 8: 90%\n (Using difference cover)\n bucket 6: 90%\n (Using difference cover)\n bucket 7: 100%\n bucket 8: 100%\n bucket 6: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) 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 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 124 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\nGetting block 12 of 60\n bucket 11: 10%\n Reserving size (126) for bucket 12\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 Calculating Z arrays for bucket 12\n bucket 11: 80%\n bucket 11: 90%\n Entering block accumulator loop for bucket 12:\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\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 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n Entering block accumulator loop for bucket 14:\n bucket 13: 20%\n bucket 14: 10%\n bucket 13: 30%\n bucket 14: 20%\n bucket 13: 40%\n bucket 14: 30%\n bucket 14: 40%\n bucket 13: 50%\n bucket 14: 50%\n bucket 13: 60%\n bucket 14: 60%\n bucket 13: 70%\n bucket 14: 70%\n bucket 13: 80%\n bucket 14: 80%\n bucket 13: 90%\n bucket 14: 90%\n bucket 13: 100%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n bucket 15: 20%\n Calculating Z arrays for bucket 16\n bucket 15: 30%\n bucket 15: 40%\n Entering block accumulator loop for bucket 16:\n bucket 15: 50%\n bucket 15: 60%\n bucket 16: 10%\n bucket 15: 70%\n bucket 16: 20%\n bucket 15: 80%\n bucket 16: 30%\n bucket 15: 90%\n bucket 16: 40%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\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 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) 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%\nGetting block 18 of 60\n bucket 17: 80%\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 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 bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) 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 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) 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 97 for bucket 20\n (Using difference cover)\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\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 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 23: 20%\n bucket 22: 30%\n bucket 23: 30%\n bucket 22: 40%\n bucket 23: 40%\n bucket 22: 50%\n bucket 23: 50%\n bucket 22: 60%\n bucket 23: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 23: 70%\n bucket 22: 90%\n bucket 23: 80%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) 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 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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 25: 20%\n bucket 26: 10%\n bucket 25: 30%\n bucket 25: 40%\n bucket 26: 20%\n bucket 25: 50%\n bucket 25: 60%\n bucket 26: 30%\n bucket 25: 70%\n bucket 25: 80%\n bucket 26: 40%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\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 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) 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%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n bucket 27: 90%\n Calculating Z arrays for bucket 28\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\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 Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\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 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 30:\n bucket 29: 10%\n bucket 30: 10%\n bucket 29: 20%\n bucket 30: 20%\n bucket 29: 30%\n bucket 30: 30%\n bucket 29: 40%\n bucket 30: 40%\n bucket 29: 50%\n bucket 30: 50%\n bucket 29: 60%\n bucket 30: 60%\n bucket 29: 70%\n bucket 30: 70%\n bucket 29: 80%\n bucket 30: 80%\n bucket 29: 90%\n bucket 30: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 31: 30%\n bucket 32: 10%\n bucket 31: 40%\n bucket 31: 50%\n bucket 32: 20%\n bucket 31: 60%\n bucket 31: 70%\n bucket 32: 30%\n bucket 31: 80%\n bucket 32: 40%\n bucket 31: 90%\n bucket 32: 50%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Entering block accumulator loop for bucket 37:\n bucket 36: 70%\n Reserving size (126) for bucket 38\n bucket 37: 10%\n Calculating Z arrays for bucket 38\n bucket 36: 80%\n bucket 37: 20%\n bucket 37: 30%\n Entering block accumulator loop for bucket 38:\n bucket 36: 90%\n bucket 37: 40%\n bucket 38: 10%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n bucket 38: 20%\n (Using difference cover)\n bucket 37: 50%\n bucket 38: 30%\n bucket 37: 60%\n bucket 38: 40%\n bucket 37: 70%\n bucket 38: 50%\n bucket 37: 80%\n bucket 38: 60%\n bucket 37: 90%\n bucket 38: 70%\n bucket 37: 100%\n bucket 38: 80%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 90%\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\nGetting block 40 of 60\n Calculating Z arrays for bucket 39\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 39: 30%\n bucket 40: 20%\n bucket 39: 40%\n bucket 40: 30%\n bucket 39: 50%\n bucket 40: 40%\n bucket 39: 60%\n bucket 40: 50%\n bucket 39: 70%\n bucket 39: 80%\n bucket 40: 60%\n bucket 39: 90%\n bucket 40: 70%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 40%\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n bucket 42: 50%\n Entering block accumulator loop for bucket 43:\n bucket 42: 60%\n Entering block accumulator loop for bucket 44:\n bucket 43: 10%\n bucket 42: 70%\n bucket 44: 10%\n bucket 43: 20%\n bucket 42: 80%\n bucket 44: 20%\n bucket 43: 30%\n bucket 44: 30%\n bucket 43: 40%\n bucket 42: 90%\n bucket 44: 40%\n bucket 43: 50%\n bucket 42: 100%\n bucket 43: 60%\n Sorting block of length 119 for bucket 42\n bucket 44: 50%\n (Using difference cover)\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 43: 90%\n bucket 44: 80%\n bucket 43: 100%\n bucket 44: 90%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\nGetting block 46 of 60\n Reserving size (126) for bucket 45\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 45\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 46:\n bucket 45: 10%\n bucket 45: 20%\n bucket 46: 10%\n bucket 45: 30%\n bucket 46: 20%\n bucket 45: 40%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 40%\n bucket 45: 90%\n bucket 45: 100%\n bucket 46: 50%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n Entering block accumulator loop for bucket 48:\n bucket 47: 20%\n bucket 48: 10%\n bucket 47: 30%\n bucket 48: 20%\n bucket 47: 40%\n bucket 48: 30%\n bucket 47: 50%\n bucket 48: 40%\n bucket 47: 60%\n bucket 48: 50%\n bucket 47: 70%\n bucket 48: 60%\n bucket 47: 80%\n bucket 48: 70%\n bucket 47: 90%\n bucket 48: 80%\n bucket 47: 100%\n bucket 48: 90%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n bucket 50: 20%\n Calculating Z arrays for bucket 51\n bucket 50: 30%\n Entering block accumulator loop for bucket 51:\n bucket 50: 40%\n bucket 51: 10%\nGetting block 52 of 60\n bucket 51: 20%\n bucket 50: 50%\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 50: 60%\n bucket 51: 30%\n bucket 50: 70%\n bucket 51: 40%\n Entering block accumulator loop for bucket 52:\n bucket 50: 80%\n bucket 51: 50%\n bucket 52: 10%\n bucket 50: 90%\n bucket 51: 60%\n bucket 52: 20%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 70%\n bucket 52: 30%\n bucket 51: 80%\n bucket 52: 40%\n bucket 51: 90%\n bucket 52: 50%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n Entering block accumulator loop for bucket 54:\n bucket 53: 20%\n bucket 54: 10%\n bucket 54: 20%\n bucket 53: 30%\n bucket 54: 30%\n bucket 53: 40%\n bucket 54: 40%\n bucket 54: 50%\n bucket 53: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 53: 60%\n bucket 54: 80%\n bucket 54: 90%\n bucket 53: 70%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n Entering block accumulator loop for bucket 58:\n bucket 57: 10%\n bucket 58: 10%\n bucket 58: 20%\n bucket 57: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 57: 30%\n bucket 58: 50%\n bucket 57: 40%\n bucket 58: 60%\n bucket 58: 70%\n bucket 57: 50%\n bucket 58: 80%\n bucket 57: 60%\n bucket 58: 90%\n bucket 57: 70%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 59: 20%\n bucket 60: 20%\n bucket 60: 30%\n bucket 59: 30%\n bucket 60: 40%\n bucket 59: 40%\n bucket 60: 50%\n bucket 59: 50%\n bucket 60: 60%\n bucket 59: 60%\n bucket 60: 70%\n bucket 59: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:41:31", "plugin": "core", "name": "end_epoch", "raw_value": "1736862091.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:41:30", "plugin": "core", "name": "start_epoch", "raw_value": "1736862090.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 33.41667604446411, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "8e1fb2a00afb225c"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "d039044e5abe6068"}, "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": "3ae98378546d9ae1", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:42:14.193810", "create_time": "2025-01-14T13:42:00.694814", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-r55jc", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/f/3/2/dataset_f324a4cf-db86-4c68-a1f6-67a86a55c701.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/a/4/b/dataset_a4b303ba-3751-4dec-aa4d-afbda39b77c7.dat' input_f.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -U 'input_f.fastq' --rna-strandness R --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000 --novel-splicesite-outfile '/galaxy/server/database/objects/2/8/2/dataset_2824a0bb-67ac-41ef-95c4-d5fc4df833f5.dat' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/8/f/1/dataset_8f1ee8fd-9d47-449d-9c6d-da84de2b0731.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\": 253, \"src\": \"hda\"}]}, \"rna_strandness\": \"R\", \"type\": \"single\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 252, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "8e1fb2a00afb225c", "src": "hda", "uuid": "f324a4cf-db86-4c68-a1f6-67a86a55c701"}, "library|input_1": {"id": "d039044e5abe6068", "src": "hda", "uuid": "a4b303ba-3751-4dec-aa4d-afbda39b77c7"}}, "outputs": {"output_alignments": {"id": "9d6289253543906e", "src": "hda", "uuid": "8f1ee8fd-9d47-449d-9c6d-da84de2b0731"}, "novel_splicesite_output": {"id": "486e4b63e691a67c", "src": "hda", "uuid": "2824a0bb-67ac-41ef-95c4-d5fc4df833f5"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n bucket 1: 10%\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 3:\nGetting block 5 of 60\n bucket 3: 10%\n bucket 1: 20%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 4\n bucket 3: 20%\n bucket 1: 30%\n bucket 3: 30%\n Calculating Z arrays for bucket 6\n bucket 3: 40%\n bucket 1: 40%\nGetting block 7 of 60\n bucket 1: 50%\n Reserving size (126) for bucket 7\n Reserving size (126) for bucket 5\n bucket 3: 50%\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 5\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Entering block accumulator loop for bucket 5:\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 6:\n bucket 1: 60%\n Calculating Z arrays for bucket 8\n bucket 4: 10%\n bucket 1: 70%\n bucket 6: 10%\n bucket 3: 60%\n Entering block accumulator loop for bucket 7:\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 8:\n bucket 7: 10%\n bucket 5: 10%\n bucket 4: 20%\n bucket 3: 70%\n bucket 1: 80%\n bucket 6: 20%\n bucket 8: 10%\n bucket 2: 10%\n bucket 4: 30%\n bucket 6: 30%\n bucket 7: 20%\n bucket 4: 40%\n bucket 2: 20%\n bucket 6: 40%\n bucket 3: 80%\n bucket 4: 50%\n bucket 7: 30%\n bucket 8: 20%\n bucket 2: 30%\n bucket 5: 20%\n bucket 7: 40%\n bucket 8: 30%\n bucket 1: 90%\n bucket 4: 60%\n bucket 3: 90%\n bucket 5: 30%\n bucket 1: 100%\n bucket 8: 40%\n bucket 4: 70%\n bucket 5: 40%\n bucket 6: 50%\n bucket 4: 80%\n bucket 8: 50%\n bucket 3: 100%\n bucket 7: 50%\n bucket 4: 90%\n bucket 5: 50%\n bucket 7: 60%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 4: 100%\n bucket 8: 60%\n bucket 6: 60%\n bucket 5: 60%\n Sorting block of length 68 for bucket 4\n bucket 2: 40%\n bucket 6: 70%\n bucket 7: 70%\n bucket 8: 70%\n Sorting block of length 42 for bucket 1\n bucket 5: 70%\n bucket 7: 80%\n bucket 6: 80%\n bucket 2: 50%\n (Using difference cover)\n bucket 5: 80%\n bucket 7: 90%\n bucket 6: 90%\n bucket 2: 60%\n bucket 5: 90%\n bucket 7: 100%\n bucket 2: 70%\n (Using difference cover)\n bucket 8: 80%\n bucket 5: 100%\n bucket 6: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 90%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 2: 80%\n bucket 2: 90%\n bucket 2: 100%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n Entering block accumulator loop for bucket 10:\n bucket 9: 30%\n bucket 10: 10%\n bucket 9: 40%\n bucket 10: 20%\n bucket 9: 50%\n bucket 10: 30%\n bucket 9: 60%\n bucket 10: 40%\n bucket 9: 70%\n bucket 10: 50%\n bucket 9: 80%\n bucket 10: 60%\n bucket 9: 90%\n bucket 10: 70%\n bucket 9: 100%\n bucket 10: 80%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 11\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n Entering block accumulator loop for bucket 11:\n bucket 12: 20%\n bucket 11: 10%\n bucket 12: 30%\n bucket 11: 20%\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 11: 70%\n bucket 12: 90%\n bucket 11: 80%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\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 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 Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n Entering block accumulator loop for bucket 16:\n bucket 15: 50%\n bucket 15: 60%\n bucket 16: 10%\n bucket 15: 70%\n bucket 15: 80%\n bucket 16: 20%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\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 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) 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 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 60%\n bucket 17: 70%\n Entering block accumulator loop for bucket 18:\n bucket 17: 80%\n bucket 17: 90%\n bucket 18: 10%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\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 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Entering block accumulator loop for bucket 19:\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n bucket 19: 70%\n bucket 20: 50%\n bucket 19: 80%\n bucket 20: 60%\n bucket 19: 90%\n bucket 20: 70%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n bucket 20: 80%\n (Using difference cover)\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\nGetting block 22 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Reserving size (126) for bucket 22\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 21: 10%\n bucket 22: 10%\n bucket 21: 20%\n bucket 22: 20%\n bucket 21: 30%\n bucket 22: 30%\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 22: 50%\n bucket 21: 60%\n bucket 22: 60%\n bucket 21: 70%\n bucket 22: 70%\n bucket 21: 80%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n bucket 22: 100%\n (Using difference cover)\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\nGetting block 24 of 60\n Calculating Z arrays for bucket 23\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n Entering block accumulator loop for bucket 24:\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 bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\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 66 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\nGetting block 28 of 60\n bucket 27: 10%\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 20%\n bucket 27: 30%\n Entering block accumulator loop for bucket 28:\n bucket 27: 40%\n bucket 28: 10%\n bucket 27: 50%\n bucket 28: 20%\n bucket 27: 60%\n bucket 28: 30%\n bucket 27: 70%\n bucket 28: 40%\n bucket 27: 80%\n bucket 28: 50%\n bucket 27: 90%\n bucket 28: 60%\n bucket 27: 100%\n bucket 28: 70%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 30: 10%\n bucket 29: 30%\n bucket 30: 20%\n bucket 29: 40%\n bucket 30: 30%\n bucket 29: 50%\n bucket 30: 40%\n bucket 29: 60%\n bucket 30: 50%\n bucket 29: 70%\n bucket 30: 60%\n bucket 29: 80%\n bucket 30: 70%\n bucket 29: 90%\n bucket 30: 80%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 32: 10%\n bucket 31: 50%\n bucket 32: 20%\n bucket 31: 60%\n bucket 31: 70%\n bucket 32: 30%\n bucket 31: 80%\n bucket 32: 40%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n bucket 32: 50%\n (Using difference cover)\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 33:\n Entering block accumulator loop for bucket 34:\n bucket 33: 10%\n bucket 34: 10%\n bucket 33: 20%\n bucket 34: 20%\n bucket 33: 30%\n bucket 34: 30%\n bucket 33: 40%\n bucket 34: 40%\n bucket 33: 50%\n bucket 34: 50%\n bucket 33: 60%\n bucket 34: 60%\n bucket 33: 70%\n bucket 34: 70%\n bucket 33: 80%\n bucket 34: 80%\n bucket 33: 90%\n bucket 34: 90%\n bucket 33: 100%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 10%\n bucket 37: 20%\n Entering block accumulator loop for bucket 38:\n bucket 37: 30%\n bucket 38: 10%\n bucket 37: 40%\n bucket 37: 50%\n bucket 38: 20%\n bucket 37: 60%\n bucket 38: 30%\n bucket 37: 70%\n bucket 38: 40%\n bucket 37: 80%\n bucket 38: 50%\n bucket 37: 90%\n bucket 38: 60%\n bucket 37: 100%\n bucket 38: 70%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Entering block accumulator loop for bucket 39:\n Calculating Z arrays for bucket 40\n bucket 39: 10%\n Entering block accumulator loop for bucket 40:\n bucket 39: 20%\n bucket 40: 10%\n bucket 39: 30%\n bucket 40: 20%\n bucket 39: 40%\n bucket 40: 30%\n bucket 39: 50%\n bucket 40: 40%\n bucket 39: 60%\n bucket 40: 50%\n bucket 39: 70%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 39: 80%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n Entering block accumulator loop for bucket 43:\n bucket 42: 20%\n bucket 43: 10%\n bucket 42: 30%\n bucket 42: 40%\n bucket 43: 20%\n bucket 42: 50%\n bucket 43: 30%\n bucket 42: 60%\n bucket 43: 40%\n bucket 42: 70%\n bucket 43: 50%\n bucket 42: 80%\n bucket 43: 60%\n bucket 42: 90%\n bucket 43: 70%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Entering block accumulator loop for bucket 45:\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n Entering block accumulator loop for bucket 46:\n bucket 45: 20%\n bucket 46: 10%\n bucket 45: 30%\n bucket 46: 20%\n bucket 45: 40%\n bucket 46: 30%\n bucket 45: 50%\n bucket 46: 40%\n bucket 45: 60%\n bucket 46: 50%\n bucket 45: 70%\n bucket 46: 60%\n bucket 45: 80%\n bucket 46: 70%\n bucket 45: 90%\n bucket 46: 80%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n bucket 47: 100%\n Calculating Z arrays for bucket 48\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 51:\n Entering block accumulator loop for bucket 50:\n bucket 51: 10%\n bucket 50: 10%\n bucket 51: 20%\n bucket 50: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 50: 30%\n bucket 51: 50%\n bucket 51: 60%\n bucket 50: 40%\n bucket 51: 70%\n bucket 50: 50%\n bucket 51: 80%\n bucket 50: 60%\n bucket 51: 90%\n bucket 51: 100%\n bucket 50: 70%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Entering block accumulator loop for bucket 52:\n Calculating Z arrays for bucket 53\n bucket 52: 10%\n bucket 52: 20%\n Entering block accumulator loop for bucket 53:\n bucket 52: 30%\n bucket 52: 40%\n bucket 53: 10%\n bucket 52: 50%\n bucket 53: 20%\n bucket 52: 60%\n bucket 52: 70%\n bucket 53: 30%\n bucket 52: 80%\n bucket 53: 40%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 56:\n bucket 55: 10%\n bucket 56: 10%\n bucket 55: 20%\n bucket 56: 20%\n bucket 55: 30%\n bucket 56: 30%\n bucket 56: 40%\n bucket 55: 40%\n bucket 56: 50%\n bucket 55: 50%\n bucket 56: 60%\n bucket 55: 60%\n bucket 56: 70%\n bucket 55: 70%\n bucket 56: 80%\n bucket 55: 80%\n bucket 56: 90%\n bucket 55: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n Entering block accumulator loop for bucket 59:\n bucket 58: 40%\n bucket 58: 50%\n bucket 59: 10%\n bucket 58: 60%\n bucket 58: 70%\n bucket 59: 20%\n bucket 58: 80%\n bucket 58: 90%\n bucket 59: 30%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n bucket 1: 10%\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 3:\nGetting block 5 of 60\n bucket 3: 10%\n bucket 1: 20%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 4\n bucket 3: 20%\n bucket 1: 30%\n bucket 3: 30%\n Calculating Z arrays for bucket 6\n bucket 3: 40%\n bucket 1: 40%\nGetting block 7 of 60\n bucket 1: 50%\n Reserving size (126) for bucket 7\n Reserving size (126) for bucket 5\n bucket 3: 50%\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 5\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Entering block accumulator loop for bucket 5:\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 6:\n bucket 1: 60%\n Calculating Z arrays for bucket 8\n bucket 4: 10%\n bucket 1: 70%\n bucket 6: 10%\n bucket 3: 60%\n Entering block accumulator loop for bucket 7:\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 8:\n bucket 7: 10%\n bucket 5: 10%\n bucket 4: 20%\n bucket 3: 70%\n bucket 1: 80%\n bucket 6: 20%\n bucket 8: 10%\n bucket 2: 10%\n bucket 4: 30%\n bucket 6: 30%\n bucket 7: 20%\n bucket 4: 40%\n bucket 2: 20%\n bucket 6: 40%\n bucket 3: 80%\n bucket 4: 50%\n bucket 7: 30%\n bucket 8: 20%\n bucket 2: 30%\n bucket 5: 20%\n bucket 7: 40%\n bucket 8: 30%\n bucket 1: 90%\n bucket 4: 60%\n bucket 3: 90%\n bucket 5: 30%\n bucket 1: 100%\n bucket 8: 40%\n bucket 4: 70%\n bucket 5: 40%\n bucket 6: 50%\n bucket 4: 80%\n bucket 8: 50%\n bucket 3: 100%\n bucket 7: 50%\n bucket 4: 90%\n bucket 5: 50%\n bucket 7: 60%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 4: 100%\n bucket 8: 60%\n bucket 6: 60%\n bucket 5: 60%\n Sorting block of length 68 for bucket 4\n bucket 2: 40%\n bucket 6: 70%\n bucket 7: 70%\n bucket 8: 70%\n Sorting block of length 42 for bucket 1\n bucket 5: 70%\n bucket 7: 80%\n bucket 6: 80%\n bucket 2: 50%\n (Using difference cover)\n bucket 5: 80%\n bucket 7: 90%\n bucket 6: 90%\n bucket 2: 60%\n bucket 5: 90%\n bucket 7: 100%\n bucket 2: 70%\n (Using difference cover)\n bucket 8: 80%\n bucket 5: 100%\n bucket 6: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 90%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 2: 80%\n bucket 2: 90%\n bucket 2: 100%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n Entering block accumulator loop for bucket 10:\n bucket 9: 30%\n bucket 10: 10%\n bucket 9: 40%\n bucket 10: 20%\n bucket 9: 50%\n bucket 10: 30%\n bucket 9: 60%\n bucket 10: 40%\n bucket 9: 70%\n bucket 10: 50%\n bucket 9: 80%\n bucket 10: 60%\n bucket 9: 90%\n bucket 10: 70%\n bucket 9: 100%\n bucket 10: 80%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 11\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n Entering block accumulator loop for bucket 11:\n bucket 12: 20%\n bucket 11: 10%\n bucket 12: 30%\n bucket 11: 20%\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 11: 70%\n bucket 12: 90%\n bucket 11: 80%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\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 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 Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n Entering block accumulator loop for bucket 16:\n bucket 15: 50%\n bucket 15: 60%\n bucket 16: 10%\n bucket 15: 70%\n bucket 15: 80%\n bucket 16: 20%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\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 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) 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 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 60%\n bucket 17: 70%\n Entering block accumulator loop for bucket 18:\n bucket 17: 80%\n bucket 17: 90%\n bucket 18: 10%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\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 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Entering block accumulator loop for bucket 19:\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n bucket 19: 70%\n bucket 20: 50%\n bucket 19: 80%\n bucket 20: 60%\n bucket 19: 90%\n bucket 20: 70%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n bucket 20: 80%\n (Using difference cover)\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\nGetting block 22 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Reserving size (126) for bucket 22\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 21: 10%\n bucket 22: 10%\n bucket 21: 20%\n bucket 22: 20%\n bucket 21: 30%\n bucket 22: 30%\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 22: 50%\n bucket 21: 60%\n bucket 22: 60%\n bucket 21: 70%\n bucket 22: 70%\n bucket 21: 80%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n bucket 22: 100%\n (Using difference cover)\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\nGetting block 24 of 60\n Calculating Z arrays for bucket 23\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n Entering block accumulator loop for bucket 24:\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 bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\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 66 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\nGetting block 28 of 60\n bucket 27: 10%\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 20%\n bucket 27: 30%\n Entering block accumulator loop for bucket 28:\n bucket 27: 40%\n bucket 28: 10%\n bucket 27: 50%\n bucket 28: 20%\n bucket 27: 60%\n bucket 28: 30%\n bucket 27: 70%\n bucket 28: 40%\n bucket 27: 80%\n bucket 28: 50%\n bucket 27: 90%\n bucket 28: 60%\n bucket 27: 100%\n bucket 28: 70%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 30: 10%\n bucket 29: 30%\n bucket 30: 20%\n bucket 29: 40%\n bucket 30: 30%\n bucket 29: 50%\n bucket 30: 40%\n bucket 29: 60%\n bucket 30: 50%\n bucket 29: 70%\n bucket 30: 60%\n bucket 29: 80%\n bucket 30: 70%\n bucket 29: 90%\n bucket 30: 80%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 32: 10%\n bucket 31: 50%\n bucket 32: 20%\n bucket 31: 60%\n bucket 31: 70%\n bucket 32: 30%\n bucket 31: 80%\n bucket 32: 40%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n bucket 32: 50%\n (Using difference cover)\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 33:\n Entering block accumulator loop for bucket 34:\n bucket 33: 10%\n bucket 34: 10%\n bucket 33: 20%\n bucket 34: 20%\n bucket 33: 30%\n bucket 34: 30%\n bucket 33: 40%\n bucket 34: 40%\n bucket 33: 50%\n bucket 34: 50%\n bucket 33: 60%\n bucket 34: 60%\n bucket 33: 70%\n bucket 34: 70%\n bucket 33: 80%\n bucket 34: 80%\n bucket 33: 90%\n bucket 34: 90%\n bucket 33: 100%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 10%\n bucket 37: 20%\n Entering block accumulator loop for bucket 38:\n bucket 37: 30%\n bucket 38: 10%\n bucket 37: 40%\n bucket 37: 50%\n bucket 38: 20%\n bucket 37: 60%\n bucket 38: 30%\n bucket 37: 70%\n bucket 38: 40%\n bucket 37: 80%\n bucket 38: 50%\n bucket 37: 90%\n bucket 38: 60%\n bucket 37: 100%\n bucket 38: 70%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Entering block accumulator loop for bucket 39:\n Calculating Z arrays for bucket 40\n bucket 39: 10%\n Entering block accumulator loop for bucket 40:\n bucket 39: 20%\n bucket 40: 10%\n bucket 39: 30%\n bucket 40: 20%\n bucket 39: 40%\n bucket 40: 30%\n bucket 39: 50%\n bucket 40: 40%\n bucket 39: 60%\n bucket 40: 50%\n bucket 39: 70%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 39: 80%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n Entering block accumulator loop for bucket 43:\n bucket 42: 20%\n bucket 43: 10%\n bucket 42: 30%\n bucket 42: 40%\n bucket 43: 20%\n bucket 42: 50%\n bucket 43: 30%\n bucket 42: 60%\n bucket 43: 40%\n bucket 42: 70%\n bucket 43: 50%\n bucket 42: 80%\n bucket 43: 60%\n bucket 42: 90%\n bucket 43: 70%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Entering block accumulator loop for bucket 45:\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n Entering block accumulator loop for bucket 46:\n bucket 45: 20%\n bucket 46: 10%\n bucket 45: 30%\n bucket 46: 20%\n bucket 45: 40%\n bucket 46: 30%\n bucket 45: 50%\n bucket 46: 40%\n bucket 45: 60%\n bucket 46: 50%\n bucket 45: 70%\n bucket 46: 60%\n bucket 45: 80%\n bucket 46: 70%\n bucket 45: 90%\n bucket 46: 80%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n bucket 47: 100%\n Calculating Z arrays for bucket 48\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 51:\n Entering block accumulator loop for bucket 50:\n bucket 51: 10%\n bucket 50: 10%\n bucket 51: 20%\n bucket 50: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 50: 30%\n bucket 51: 50%\n bucket 51: 60%\n bucket 50: 40%\n bucket 51: 70%\n bucket 50: 50%\n bucket 51: 80%\n bucket 50: 60%\n bucket 51: 90%\n bucket 51: 100%\n bucket 50: 70%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Entering block accumulator loop for bucket 52:\n Calculating Z arrays for bucket 53\n bucket 52: 10%\n bucket 52: 20%\n Entering block accumulator loop for bucket 53:\n bucket 52: 30%\n bucket 52: 40%\n bucket 53: 10%\n bucket 52: 50%\n bucket 53: 20%\n bucket 52: 60%\n bucket 52: 70%\n bucket 53: 30%\n bucket 52: 80%\n bucket 53: 40%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 56:\n bucket 55: 10%\n bucket 56: 10%\n bucket 55: 20%\n bucket 56: 20%\n bucket 55: 30%\n bucket 56: 30%\n bucket 56: 40%\n bucket 55: 40%\n bucket 56: 50%\n bucket 55: 50%\n bucket 56: 60%\n bucket 55: 60%\n bucket 56: 70%\n bucket 55: 70%\n bucket 56: 80%\n bucket 55: 80%\n bucket 56: 90%\n bucket 55: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n Entering block accumulator loop for bucket 59:\n bucket 58: 40%\n bucket 58: 50%\n bucket 59: 10%\n bucket 58: 60%\n bucket 58: 70%\n bucket 59: 20%\n bucket 58: 80%\n bucket 58: 90%\n bucket 59: 30%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:42:03", "plugin": "core", "name": "end_epoch", "raw_value": "1736862123.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:42:03", "plugin": "core", "name": "start_epoch", "raw_value": "1736862123.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 29.44083046913147, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "55b3f17755221fd8"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "f5d438bd64aea3a8"}, "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": "7d67a45280f2c02b", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:42:44.656682", "create_time": "2025-01-14T13:42:32.671315", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-t7bmj", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/a/1/b/dataset_a1b63240-f254-4c51-976e-07cae7da0258.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && bzcat '/galaxy/server/database/objects/7/1/e/dataset_71e79b14-1594-4bca-b4fa-d6da01255f7f.dat' | seqtk seq -1 /dev/stdin > input_f.fastq && bzcat '/galaxy/server/database/objects/7/1/e/dataset_71e79b14-1594-4bca-b4fa-d6da01255f7f.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/8/7/2/dataset_872243fc-b2df-4df5-b942-817526efb72e.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\": 257, \"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\": 256, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "55b3f17755221fd8", "src": "hda", "uuid": "a1b63240-f254-4c51-976e-07cae7da0258"}, "library|input_1": {"id": "f5d438bd64aea3a8", "src": "hda", "uuid": "71e79b14-1594-4bca-b4fa-d6da01255f7f"}}, "outputs": {"output_alignments": {"id": "2cbd5b2ab946873e", "src": "hda", "uuid": "872243fc-b2df-4df5-b942-817526efb72e"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n bucket 1: 10%\n bucket 1: 20%\nGetting block 3 of 60\n bucket 1: 30%\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\n bucket 1: 40%\n Calculating Z arrays for bucket 3\n bucket 2: 10%\n bucket 1: 50%\n bucket 1: 60%\n bucket 2: 20%\nGetting block 4 of 60\n bucket 1: 70%\n bucket 2: 30%\n Entering block accumulator loop for bucket 3:\n bucket 1: 80%\n bucket 2: 40%\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n bucket 2: 50%\n Reserving size (126) for bucket 5\n bucket 3: 10%\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 4\n bucket 2: 60%\n bucket 1: 90%\n bucket 3: 20%\n bucket 2: 70%\n bucket 1: 100%\n Entering block accumulator loop for bucket 5:\n bucket 2: 80%\n bucket 3: 30%\n Sorting block of length 42 for bucket 1\n bucket 2: 90%\n (Using difference cover)\n bucket 5: 10%\n Entering block accumulator loop for bucket 4:\n bucket 3: 40%\n bucket 5: 20%\n bucket 2: 100%\n bucket 3: 50%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 5: 30%\n bucket 4: 10%\nGetting block 7 of 60\n bucket 3: 60%\n bucket 5: 40%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 3: 70%\n Reserving size (126) for bucket 7\n bucket 4: 20%\n Calculating Z arrays for bucket 7\n bucket 5: 50%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 5: 60%\n Entering block accumulator loop for bucket 7:\n bucket 5: 70%\n bucket 3: 80%\n bucket 5: 80%\n Calculating Z arrays for bucket 6\n Sorting block time: 00:00:00\n bucket 5: 90%\n bucket 4: 30%\n bucket 5: 100%\n bucket 3: 90%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\nReturning block of 43 for bucket 1\n bucket 7: 10%\n Entering block accumulator loop for bucket 6:\n bucket 3: 100%\n bucket 4: 40%\n bucket 7: 20%\n Sorting block of length 106 for bucket 3\n bucket 4: 50%\n (Using difference cover)\n bucket 7: 30%\n bucket 6: 10%\n bucket 4: 60%\n bucket 7: 40%\n Calculating Z arrays for bucket 8\n bucket 6: 20%\n bucket 7: 50%\n bucket 4: 70%\n bucket 7: 60%\n bucket 4: 80%\n bucket 7: 70%\n bucket 4: 90%\n bucket 6: 30%\n bucket 7: 80%\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 7: 90%\n bucket 6: 40%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\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 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\nGetting block 10 of 60\n Calculating Z arrays for bucket 9\n Reserving size (126) for bucket 10\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 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 124 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\nGetting block 13 of 60\n bucket 12: 20%\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 11:\n bucket 12: 30%\n Entering block accumulator loop for bucket 13:\n bucket 12: 40%\n bucket 11: 10%\n bucket 12: 50%\n bucket 13: 10%\n bucket 11: 20%\n bucket 12: 60%\n bucket 13: 20%\n bucket 11: 30%\n bucket 12: 70%\n bucket 13: 30%\n bucket 11: 40%\n bucket 12: 80%\n bucket 13: 40%\n bucket 11: 50%\n bucket 12: 90%\n bucket 13: 50%\n bucket 11: 60%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n bucket 13: 60%\n (Using difference cover)\n bucket 11: 70%\n bucket 13: 70%\n bucket 11: 80%\n bucket 13: 80%\n bucket 11: 90%\n bucket 13: 90%\n bucket 11: 100%\n bucket 13: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) 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 82 for bucket 14\n (Using difference cover)\nGetting block 15 of 60\n Reserving size (126) 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 Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\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 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) 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 100 for bucket 16\n (Using difference cover)\nGetting block 17 of 60\n Reserving size (126) 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 60\n Reserving size (126) 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 Sorting block time: 00:00:00\n bucket 18: 10%\nReturning block of 101 for bucket 16\n bucket 17: 50%\n bucket 18: 20%\n bucket 17: 60%\n bucket 18: 30%\n bucket 18: 40%\n bucket 17: 70%\n bucket 18: 50%\n bucket 17: 80%\n bucket 18: 60%\n bucket 17: 90%\n bucket 18: 70%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Entering block accumulator loop for bucket 19:\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n bucket 20: 50%\n bucket 19: 70%\n bucket 20: 60%\n bucket 19: 80%\n bucket 20: 70%\n bucket 19: 90%\n bucket 20: 80%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) 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%\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n bucket 21: 70%\n Calculating Z arrays for bucket 22\n bucket 21: 80%\n Entering block accumulator loop for bucket 22:\n bucket 21: 90%\n bucket 22: 10%\n bucket 21: 100%\n Sorting block of length 54 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 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Entering block accumulator loop for bucket 23:\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 10%\n bucket 23: 20%\n Entering block accumulator loop for bucket 24:\n bucket 23: 30%\n bucket 23: 40%\n bucket 24: 10%\n bucket 23: 50%\n bucket 24: 20%\n bucket 23: 60%\n bucket 24: 30%\n bucket 23: 70%\n bucket 24: 40%\n bucket 23: 80%\n bucket 24: 50%\n bucket 23: 90%\n bucket 24: 60%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n Entering block accumulator loop for bucket 26:\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 25: 50%\n bucket 26: 40%\n bucket 25: 60%\n bucket 26: 50%\n bucket 25: 70%\n bucket 26: 60%\n bucket 25: 80%\n bucket 26: 70%\n bucket 25: 90%\n bucket 26: 80%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 27 of 60\n Reserving size (126) 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%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 70%\n bucket 27: 80%\n Entering block accumulator loop for bucket 28:\n bucket 27: 90%\n bucket 28: 10%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\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 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Entering block accumulator loop for bucket 29:\n Calculating Z arrays for bucket 30\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 30: 10%\n bucket 29: 30%\n bucket 30: 20%\n bucket 29: 40%\n bucket 30: 30%\n bucket 29: 50%\n bucket 30: 40%\n bucket 29: 60%\n bucket 30: 50%\n bucket 29: 70%\n bucket 30: 60%\n bucket 29: 80%\n bucket 30: 70%\n bucket 29: 90%\n bucket 30: 80%\n bucket 29: 100%\n bucket 30: 90%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n bucket 32: 30%\n bucket 32: 40%\n bucket 32: 50%\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\nGetting block 35 of 60\n bucket 34: 10%\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 20%\n Entering block accumulator loop for bucket 35:\n bucket 34: 30%\n bucket 35: 10%\n bucket 34: 40%\n bucket 35: 20%\n bucket 35: 30%\n bucket 34: 50%\n bucket 35: 40%\n bucket 34: 60%\n bucket 35: 50%\n bucket 35: 60%\n bucket 34: 70%\n bucket 35: 70%\n bucket 34: 80%\n bucket 35: 80%\n bucket 35: 90%\n bucket 34: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 36:\n Entering block accumulator loop for bucket 37:\n bucket 36: 10%\n bucket 37: 10%\n bucket 36: 20%\n bucket 37: 20%\n bucket 36: 30%\n bucket 37: 30%\n bucket 36: 40%\n bucket 37: 40%\n bucket 36: 50%\n bucket 37: 50%\n bucket 36: 60%\n bucket 37: 60%\n bucket 36: 70%\n bucket 37: 70%\n bucket 37: 80%\n bucket 36: 80%\n bucket 37: 90%\n bucket 36: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n bucket 39: 30%\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 39: 40%\n bucket 40: 10%\n bucket 39: 50%\n bucket 40: 20%\n bucket 39: 60%\n bucket 40: 30%\n bucket 39: 70%\n bucket 40: 40%\n bucket 39: 80%\n bucket 40: 50%\n bucket 39: 90%\n bucket 40: 60%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 41:\n bucket 42: 10%\n bucket 41: 10%\n bucket 42: 20%\n bucket 41: 20%\n bucket 42: 30%\n bucket 41: 30%\n bucket 42: 40%\n bucket 41: 40%\n bucket 42: 50%\n bucket 41: 50%\n bucket 42: 60%\n bucket 41: 60%\n bucket 42: 70%\n bucket 41: 70%\n bucket 42: 80%\n bucket 41: 80%\n bucket 42: 90%\n bucket 41: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 60\n Entering block accumulator loop for bucket 44:\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 10%\n bucket 44: 20%\n Entering block accumulator loop for bucket 45:\n bucket 44: 30%\n bucket 44: 40%\n bucket 45: 10%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 45: 20%\n bucket 44: 80%\n bucket 44: 90%\n bucket 45: 30%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\nGetting block 47 of 60\n bucket 46: 50%\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 60%\n bucket 46: 70%\n Entering block accumulator loop for bucket 47:\n bucket 46: 80%\n bucket 46: 90%\n bucket 47: 10%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\nGetting block 50 of 60\n Entering block accumulator loop for bucket 49:\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 49: 30%\n bucket 49: 40%\n bucket 50: 10%\n bucket 49: 50%\n bucket 50: 20%\n bucket 49: 60%\n bucket 50: 30%\n bucket 49: 70%\n bucket 50: 40%\n bucket 49: 80%\n bucket 50: 50%\n bucket 50: 60%\n bucket 49: 90%\n bucket 50: 70%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\nGetting block 52 of 60\n bucket 51: 10%\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 20%\n bucket 51: 30%\n Entering block accumulator loop for bucket 52:\n bucket 51: 40%\n bucket 52: 10%\n bucket 51: 50%\n bucket 52: 20%\n bucket 51: 60%\n bucket 52: 30%\n bucket 51: 70%\n bucket 52: 40%\n bucket 51: 80%\n bucket 52: 50%\n bucket 51: 90%\n bucket 52: 60%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 70%\n bucket 54: 80%\n Entering block accumulator loop for bucket 55:\n bucket 54: 90%\n bucket 54: 100%\n bucket 55: 10%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n bucket 56: 20%\n Calculating Z arrays for bucket 57\n bucket 56: 30%\n Entering block accumulator loop for bucket 57:\n bucket 56: 40%\n bucket 57: 10%\n bucket 56: 50%\n bucket 57: 20%\n bucket 56: 60%\n bucket 57: 30%\n bucket 56: 70%\n bucket 57: 40%\n bucket 56: 80%\n bucket 57: 50%\n bucket 56: 90%\n bucket 57: 60%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\nGetting block 60 of 60\n bucket 59: 10%\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 20%\n Entering block accumulator loop for bucket 60:\n bucket 59: 30%\n bucket 60: 10%\n bucket 59: 40%\n bucket 60: 20%\n bucket 60: 30%\n bucket 59: 50%\n bucket 60: 40%\n bucket 59: 60%\n bucket 60: 50%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n bucket 59: 90%\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n bucket 1: 10%\n bucket 1: 20%\nGetting block 3 of 60\n bucket 1: 30%\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\n bucket 1: 40%\n Calculating Z arrays for bucket 3\n bucket 2: 10%\n bucket 1: 50%\n bucket 1: 60%\n bucket 2: 20%\nGetting block 4 of 60\n bucket 1: 70%\n bucket 2: 30%\n Entering block accumulator loop for bucket 3:\n bucket 1: 80%\n bucket 2: 40%\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n bucket 2: 50%\n Reserving size (126) for bucket 5\n bucket 3: 10%\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 4\n bucket 2: 60%\n bucket 1: 90%\n bucket 3: 20%\n bucket 2: 70%\n bucket 1: 100%\n Entering block accumulator loop for bucket 5:\n bucket 2: 80%\n bucket 3: 30%\n Sorting block of length 42 for bucket 1\n bucket 2: 90%\n (Using difference cover)\n bucket 5: 10%\n Entering block accumulator loop for bucket 4:\n bucket 3: 40%\n bucket 5: 20%\n bucket 2: 100%\n bucket 3: 50%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 5: 30%\n bucket 4: 10%\nGetting block 7 of 60\n bucket 3: 60%\n bucket 5: 40%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 3: 70%\n Reserving size (126) for bucket 7\n bucket 4: 20%\n Calculating Z arrays for bucket 7\n bucket 5: 50%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 5: 60%\n Entering block accumulator loop for bucket 7:\n bucket 5: 70%\n bucket 3: 80%\n bucket 5: 80%\n Calculating Z arrays for bucket 6\n Sorting block time: 00:00:00\n bucket 5: 90%\n bucket 4: 30%\n bucket 5: 100%\n bucket 3: 90%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\nReturning block of 43 for bucket 1\n bucket 7: 10%\n Entering block accumulator loop for bucket 6:\n bucket 3: 100%\n bucket 4: 40%\n bucket 7: 20%\n Sorting block of length 106 for bucket 3\n bucket 4: 50%\n (Using difference cover)\n bucket 7: 30%\n bucket 6: 10%\n bucket 4: 60%\n bucket 7: 40%\n Calculating Z arrays for bucket 8\n bucket 6: 20%\n bucket 7: 50%\n bucket 4: 70%\n bucket 7: 60%\n bucket 4: 80%\n bucket 7: 70%\n bucket 4: 90%\n bucket 6: 30%\n bucket 7: 80%\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 7: 90%\n bucket 6: 40%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 6: 50%\n bucket 6: 60%\n bucket 6: 70%\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\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 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\nGetting block 10 of 60\n Calculating Z arrays for bucket 9\n Reserving size (126) for bucket 10\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 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 124 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\nGetting block 13 of 60\n bucket 12: 20%\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 11:\n bucket 12: 30%\n Entering block accumulator loop for bucket 13:\n bucket 12: 40%\n bucket 11: 10%\n bucket 12: 50%\n bucket 13: 10%\n bucket 11: 20%\n bucket 12: 60%\n bucket 13: 20%\n bucket 11: 30%\n bucket 12: 70%\n bucket 13: 30%\n bucket 11: 40%\n bucket 12: 80%\n bucket 13: 40%\n bucket 11: 50%\n bucket 12: 90%\n bucket 13: 50%\n bucket 11: 60%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n bucket 13: 60%\n (Using difference cover)\n bucket 11: 70%\n bucket 13: 70%\n bucket 11: 80%\n bucket 13: 80%\n bucket 11: 90%\n bucket 13: 90%\n bucket 11: 100%\n bucket 13: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) 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 82 for bucket 14\n (Using difference cover)\nGetting block 15 of 60\n Reserving size (126) 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 Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\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 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) 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 100 for bucket 16\n (Using difference cover)\nGetting block 17 of 60\n Reserving size (126) 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 60\n Reserving size (126) 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 Sorting block time: 00:00:00\n bucket 18: 10%\nReturning block of 101 for bucket 16\n bucket 17: 50%\n bucket 18: 20%\n bucket 17: 60%\n bucket 18: 30%\n bucket 18: 40%\n bucket 17: 70%\n bucket 18: 50%\n bucket 17: 80%\n bucket 18: 60%\n bucket 17: 90%\n bucket 18: 70%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Entering block accumulator loop for bucket 19:\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n bucket 20: 50%\n bucket 19: 70%\n bucket 20: 60%\n bucket 19: 80%\n bucket 20: 70%\n bucket 19: 90%\n bucket 20: 80%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) 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%\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n bucket 21: 70%\n Calculating Z arrays for bucket 22\n bucket 21: 80%\n Entering block accumulator loop for bucket 22:\n bucket 21: 90%\n bucket 22: 10%\n bucket 21: 100%\n Sorting block of length 54 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 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Entering block accumulator loop for bucket 23:\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 10%\n bucket 23: 20%\n Entering block accumulator loop for bucket 24:\n bucket 23: 30%\n bucket 23: 40%\n bucket 24: 10%\n bucket 23: 50%\n bucket 24: 20%\n bucket 23: 60%\n bucket 24: 30%\n bucket 23: 70%\n bucket 24: 40%\n bucket 23: 80%\n bucket 24: 50%\n bucket 23: 90%\n bucket 24: 60%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n Entering block accumulator loop for bucket 26:\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 25: 50%\n bucket 26: 40%\n bucket 25: 60%\n bucket 26: 50%\n bucket 25: 70%\n bucket 26: 60%\n bucket 25: 80%\n bucket 26: 70%\n bucket 25: 90%\n bucket 26: 80%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 27 of 60\n Reserving size (126) 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%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 70%\n bucket 27: 80%\n Entering block accumulator loop for bucket 28:\n bucket 27: 90%\n bucket 28: 10%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\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 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Entering block accumulator loop for bucket 29:\n Calculating Z arrays for bucket 30\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 30: 10%\n bucket 29: 30%\n bucket 30: 20%\n bucket 29: 40%\n bucket 30: 30%\n bucket 29: 50%\n bucket 30: 40%\n bucket 29: 60%\n bucket 30: 50%\n bucket 29: 70%\n bucket 30: 60%\n bucket 29: 80%\n bucket 30: 70%\n bucket 29: 90%\n bucket 30: 80%\n bucket 29: 100%\n bucket 30: 90%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n bucket 32: 30%\n bucket 32: 40%\n bucket 32: 50%\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\nGetting block 35 of 60\n bucket 34: 10%\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 20%\n Entering block accumulator loop for bucket 35:\n bucket 34: 30%\n bucket 35: 10%\n bucket 34: 40%\n bucket 35: 20%\n bucket 35: 30%\n bucket 34: 50%\n bucket 35: 40%\n bucket 34: 60%\n bucket 35: 50%\n bucket 35: 60%\n bucket 34: 70%\n bucket 35: 70%\n bucket 34: 80%\n bucket 35: 80%\n bucket 35: 90%\n bucket 34: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 36:\n Entering block accumulator loop for bucket 37:\n bucket 36: 10%\n bucket 37: 10%\n bucket 36: 20%\n bucket 37: 20%\n bucket 36: 30%\n bucket 37: 30%\n bucket 36: 40%\n bucket 37: 40%\n bucket 36: 50%\n bucket 37: 50%\n bucket 36: 60%\n bucket 37: 60%\n bucket 36: 70%\n bucket 37: 70%\n bucket 37: 80%\n bucket 36: 80%\n bucket 37: 90%\n bucket 36: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n bucket 39: 30%\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 39: 40%\n bucket 40: 10%\n bucket 39: 50%\n bucket 40: 20%\n bucket 39: 60%\n bucket 40: 30%\n bucket 39: 70%\n bucket 40: 40%\n bucket 39: 80%\n bucket 40: 50%\n bucket 39: 90%\n bucket 40: 60%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 41:\n bucket 42: 10%\n bucket 41: 10%\n bucket 42: 20%\n bucket 41: 20%\n bucket 42: 30%\n bucket 41: 30%\n bucket 42: 40%\n bucket 41: 40%\n bucket 42: 50%\n bucket 41: 50%\n bucket 42: 60%\n bucket 41: 60%\n bucket 42: 70%\n bucket 41: 70%\n bucket 42: 80%\n bucket 41: 80%\n bucket 42: 90%\n bucket 41: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 60\n Entering block accumulator loop for bucket 44:\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 10%\n bucket 44: 20%\n Entering block accumulator loop for bucket 45:\n bucket 44: 30%\n bucket 44: 40%\n bucket 45: 10%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 45: 20%\n bucket 44: 80%\n bucket 44: 90%\n bucket 45: 30%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\nGetting block 47 of 60\n bucket 46: 50%\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 60%\n bucket 46: 70%\n Entering block accumulator loop for bucket 47:\n bucket 46: 80%\n bucket 46: 90%\n bucket 47: 10%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\nGetting block 50 of 60\n Entering block accumulator loop for bucket 49:\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 49: 30%\n bucket 49: 40%\n bucket 50: 10%\n bucket 49: 50%\n bucket 50: 20%\n bucket 49: 60%\n bucket 50: 30%\n bucket 49: 70%\n bucket 50: 40%\n bucket 49: 80%\n bucket 50: 50%\n bucket 50: 60%\n bucket 49: 90%\n bucket 50: 70%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\nGetting block 52 of 60\n bucket 51: 10%\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 20%\n bucket 51: 30%\n Entering block accumulator loop for bucket 52:\n bucket 51: 40%\n bucket 52: 10%\n bucket 51: 50%\n bucket 52: 20%\n bucket 51: 60%\n bucket 52: 30%\n bucket 51: 70%\n bucket 52: 40%\n bucket 51: 80%\n bucket 52: 50%\n bucket 51: 90%\n bucket 52: 60%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 70%\n bucket 54: 80%\n Entering block accumulator loop for bucket 55:\n bucket 54: 90%\n bucket 54: 100%\n bucket 55: 10%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n bucket 56: 20%\n Calculating Z arrays for bucket 57\n bucket 56: 30%\n Entering block accumulator loop for bucket 57:\n bucket 56: 40%\n bucket 57: 10%\n bucket 56: 50%\n bucket 57: 20%\n bucket 56: 60%\n bucket 57: 30%\n bucket 56: 70%\n bucket 57: 40%\n bucket 56: 80%\n bucket 57: 50%\n bucket 56: 90%\n bucket 57: 60%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\nGetting block 60 of 60\n bucket 59: 10%\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 20%\n Entering block accumulator loop for bucket 60:\n bucket 59: 30%\n bucket 60: 10%\n bucket 59: 40%\n bucket 60: 20%\n bucket 60: 30%\n bucket 59: 50%\n bucket 60: 40%\n bucket 59: 60%\n bucket 60: 50%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n bucket 59: 90%\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:42:34", "plugin": "core", "name": "end_epoch", "raw_value": "1736862154.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:42:34", "plugin": "core", "name": "start_epoch", "raw_value": "1736862154.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 68.60810995101929, "inputs": {"reference_genome|source": "indexed", "library|input_1": {"src": "hda", "id": "19ad8dc6a9342a2d"}, "library|input_2": {"src": "hda", "id": "3ae98378546d9ae1"}, "library|type": "paired"}, "job": {"model_class": "Job", "id": "1058bf491e452b34", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:35:37.450880", "create_time": "2025-01-14T13:34:48.110153", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-9hk26", "command_line": "set -o pipefail; ln -f -s '/galaxy/server/database/objects/2/5/7/dataset_257c0c8d-c141-47cb-81b9-8b717d7378cb.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/a/2/2/dataset_a226e572-44fd-4f2d-9d9f-c0944bd82f37.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/4/1/3/dataset_413d647e-85c8-4e06-8643-0b99366452e1.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\": 203, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 204, \"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": {"library|input_1": {"id": "19ad8dc6a9342a2d", "src": "hda", "uuid": "257c0c8d-c141-47cb-81b9-8b717d7378cb"}, "library|input_2": {"id": "3ae98378546d9ae1", "src": "hda", "uuid": "a226e572-44fd-4f2d-9d9f-c0944bd82f37"}}, "outputs": {"output_alignments": {"id": "350b5dbb40790a30", "src": "hda", "uuid": "413d647e-85c8-4e06-8643-0b99366452e1"}}, "output_collections": {}, "tool_stdout": "", "tool_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", "job_stdout": "", "job_stderr": "", "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", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "39 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "39.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:35:28", "plugin": "core", "name": "end_epoch", "raw_value": "1736861728.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:34:49", "plugin": "core", "name": "start_epoch", "raw_value": "1736861689.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "output_problems": ["Output output_alignments: different than expected, difference (using diff):\n( /tmp/local_bam_converted_to_sam_lcvnecef.sam v. /tmp/history_bam_converted_to_sam_3u4ui50l.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 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"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": 33.83154296875, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "f2a782dae4d14e94"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "7d67a45280f2c02b"}, "library|input_2": {"src": "hda", "id": "55f67d516a9b4b37"}, "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": "fd04d8a1cbe2b97a", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:36:11.161201", "create_time": "2025-01-14T13:35:59.064018", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-zz4jj", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/4/7/7/dataset_47797dec-d49f-47ec-8bee-7d4fcea5200c.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/8/d/a/dataset_8daf6f9e-a997-4683-a887-8a61c1e5bcfa.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/e/f/f/dataset_eff318a6-4865-42af-a631-e6fa087494a7.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/7/2/f/dataset_72faabdc-0234-4719-a48d-efe579b922cf.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\": 207, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 208, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 206, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "f2a782dae4d14e94", "src": "hda", "uuid": "47797dec-d49f-47ec-8bee-7d4fcea5200c"}, "library|input_1": {"id": "7d67a45280f2c02b", "src": "hda", "uuid": "8daf6f9e-a997-4683-a887-8a61c1e5bcfa"}, "library|input_2": {"id": "55f67d516a9b4b37", "src": "hda", "uuid": "eff318a6-4865-42af-a631-e6fa087494a7"}}, "outputs": {"output_alignments": {"id": "3a1f79960c96199c", "src": "hda", "uuid": "72faabdc-0234-4719-a48d-efe579b922cf"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n Reserving size (126) for bucket 3\nGetting block 5 of 60\n Reserving size (126) for bucket 5\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 5\n bucket 2: 10%\n bucket 1: 10%\n bucket 2: 20%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 5:\n Entering block accumulator loop for bucket 3:\n bucket 1: 20%\n bucket 2: 30%\n bucket 5: 10%\n bucket 2: 40%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 5: 20%\n bucket 2: 50%\n Entering block accumulator loop for bucket 4:\nGetting block 6 of 60\n bucket 2: 60%\n bucket 3: 10%\n bucket 1: 30%\n bucket 2: 70%\n Reserving size (126) for bucket 6\n bucket 4: 10%\n bucket 5: 30%\n bucket 1: 40%\n bucket 3: 20%\n Calculating Z arrays for bucket 7\n bucket 2: 80%\n Calculating Z arrays for bucket 6\n bucket 1: 50%\nGetting block 8 of 60\n Entering block accumulator loop for bucket 6:\n bucket 4: 20%\n Reserving size (126) for bucket 8\n bucket 2: 90%\n bucket 5: 40%\n bucket 6: 10%\n bucket 4: 30%\n bucket 2: 100%\n bucket 3: 30%\n bucket 5: 50%\n bucket 6: 20%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 1: 60%\n bucket 4: 40%\n bucket 3: 40%\n bucket 5: 60%\n Entering block accumulator loop for bucket 7:\n bucket 6: 30%\n Calculating Z arrays for bucket 8\n bucket 4: 50%\n bucket 5: 70%\n bucket 1: 70%\n bucket 6: 40%\n bucket 4: 60%\n bucket 5: 80%\n bucket 6: 50%\n bucket 3: 50%\n Entering block accumulator loop for bucket 8:\n bucket 1: 80%\n bucket 4: 70%\n bucket 5: 90%\n bucket 3: 60%\n bucket 7: 10%\n bucket 6: 60%\n bucket 1: 90%\n bucket 5: 100%\n bucket 4: 80%\n bucket 6: 70%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 10%\n bucket 1: 100%\n bucket 3: 70%\n bucket 7: 20%\n bucket 6: 80%\n bucket 4: 90%\n Sorting block of length 42 for bucket 1\n bucket 6: 90%\n (Using difference cover)\n bucket 3: 80%\n bucket 7: 30%\n bucket 8: 20%\n bucket 6: 100%\n bucket 3: 90%\n bucket 4: 100%\n bucket 7: 40%\n bucket 8: 30%\n bucket 3: 100%\n bucket 7: 50%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block of length 90 for bucket 6\n Sorting block time: 00:00:00\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n bucket 7: 60%\nReturning block of 85 for bucket 2\n (Using difference cover)\n bucket 8: 40%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 8: 50%\n bucket 7: 100%\n Sorting block of length 75 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 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\n Reserving size (126) for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 10:\n Entering block accumulator loop for bucket 9:\n bucket 10: 10%\n bucket 10: 20%\n bucket 9: 10%\n bucket 10: 30%\n bucket 9: 20%\n bucket 10: 40%\n bucket 9: 30%\n bucket 10: 50%\n bucket 9: 40%\n bucket 10: 60%\n bucket 9: 50%\n bucket 10: 70%\n bucket 9: 60%\n bucket 10: 80%\n bucket 9: 70%\n bucket 10: 90%\n bucket 9: 80%\n bucket 10: 100%\n bucket 9: 90%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) 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 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n Entering block accumulator loop for bucket 13:\n bucket 12: 20%\n bucket 12: 30%\n bucket 13: 10%\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 12: 60%\n bucket 13: 30%\nGetting block 14 of 60\n bucket 12: 70%\n bucket 13: 40%\n Reserving size (126) for bucket 14\n bucket 12: 80%\n Calculating Z arrays for bucket 14\n bucket 13: 50%\n bucket 12: 90%\n bucket 13: 60%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Entering block accumulator loop for bucket 14:\n bucket 13: 70%\n bucket 13: 80%\n bucket 14: 10%\n bucket 13: 90%\n bucket 14: 20%\n bucket 13: 100%\n bucket 14: 30%\n Sorting block of length 85 for bucket 13\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 time: 00:00:00\n Sorting block of length 82 for bucket 14\n (Using difference cover)\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) 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%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 30%\n bucket 15: 40%\n Entering block accumulator loop for bucket 16:\n bucket 15: 50%\n bucket 16: 10%\n bucket 15: 60%\n bucket 16: 20%\n bucket 15: 70%\n bucket 16: 30%\n bucket 15: 80%\n bucket 16: 40%\n bucket 15: 90%\n bucket 16: 50%\n bucket 15: 100%\n bucket 16: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Entering block accumulator loop for bucket 17:\n Reserving size (126) 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 bucket 18: 70%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Entering block accumulator loop for bucket 19:\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n bucket 19: 20%\n Entering block accumulator loop for bucket 20:\n bucket 19: 30%\n bucket 20: 10%\n bucket 19: 40%\n bucket 20: 20%\n bucket 19: 50%\n bucket 19: 60%\n bucket 20: 30%\n bucket 19: 70%\n bucket 20: 40%\n bucket 19: 80%\n bucket 20: 50%\n bucket 19: 90%\n bucket 20: 60%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n Entering block accumulator loop for bucket 22:\n bucket 21: 20%\n bucket 22: 10%\n bucket 21: 30%\n bucket 22: 20%\n bucket 21: 40%\n bucket 22: 30%\n bucket 21: 50%\n bucket 22: 40%\n bucket 21: 60%\n bucket 22: 50%\n bucket 21: 70%\n bucket 22: 60%\n bucket 21: 80%\n bucket 22: 70%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n bucket 22: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\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 24: 10%\n bucket 24: 20%\n bucket 23: 10%\n bucket 24: 30%\n bucket 23: 20%\n bucket 24: 40%\n bucket 23: 30%\n bucket 24: 50%\n bucket 24: 60%\n bucket 23: 40%\n bucket 24: 70%\n bucket 23: 50%\n bucket 24: 80%\n bucket 24: 90%\n bucket 23: 60%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) 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 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n bucket 25: 50%\n bucket 25: 60%\n Entering block accumulator loop for bucket 26:\n bucket 25: 70%\n bucket 26: 10%\n bucket 25: 80%\n bucket 26: 20%\n bucket 25: 90%\n bucket 26: 30%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\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 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) 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%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 90%\n bucket 27: 100%\n Entering block accumulator loop for bucket 28:\n Sorting block of length 119 for bucket 27\n (Using difference cover)\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 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 29:\n bucket 30: 10%\n bucket 29: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 29: 20%\n bucket 30: 40%\n bucket 29: 30%\n bucket 30: 50%\n bucket 29: 40%\n bucket 30: 60%\n bucket 29: 50%\n bucket 30: 70%\n bucket 29: 60%\n bucket 30: 80%\n bucket 30: 90%\n bucket 29: 70%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 10%\n bucket 31: 20%\n Entering block accumulator loop for bucket 32:\n bucket 31: 30%\n bucket 32: 10%\n bucket 31: 40%\n bucket 32: 20%\n bucket 31: 50%\n bucket 32: 30%\n bucket 31: 60%\n bucket 32: 40%\n bucket 31: 70%\n bucket 32: 50%\n bucket 31: 80%\n bucket 32: 60%\n bucket 32: 70%\n bucket 31: 90%\n bucket 32: 80%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 34:\n Entering block accumulator loop for bucket 33:\n bucket 34: 10%\n bucket 33: 10%\n bucket 34: 20%\n bucket 33: 20%\n bucket 34: 30%\n bucket 33: 30%\n bucket 34: 40%\n bucket 33: 40%\n bucket 34: 50%\n bucket 33: 50%\n bucket 34: 60%\n bucket 33: 60%\n bucket 34: 70%\n bucket 33: 70%\n bucket 34: 80%\n bucket 33: 80%\n bucket 34: 90%\n bucket 33: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n bucket 35: 90%\n Calculating Z arrays for bucket 36\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 37:\n Entering block accumulator loop for bucket 38:\n bucket 37: 10%\n bucket 38: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 38: 20%\n bucket 37: 40%\n bucket 38: 30%\n bucket 37: 50%\n bucket 37: 60%\n bucket 38: 40%\n bucket 37: 70%\n bucket 38: 50%\n bucket 37: 80%\n bucket 37: 90%\n bucket 38: 60%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n Entering block accumulator loop for bucket 40:\n bucket 39: 20%\n bucket 40: 10%\n bucket 39: 30%\n bucket 40: 20%\n bucket 39: 40%\n bucket 40: 30%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n Sorting block time: 00:00:00\n bucket 40: 80%\nReturning block of 126 for bucket 39\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 60\n Entering block accumulator loop for bucket 41:\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 41: 10%\n Entering block accumulator loop for bucket 42:\n bucket 41: 20%\n bucket 42: 10%\n bucket 41: 30%\n bucket 42: 20%\n bucket 41: 40%\n bucket 42: 30%\n bucket 41: 50%\n bucket 42: 40%\n bucket 41: 60%\n bucket 42: 50%\n bucket 42: 60%\n bucket 41: 70%\n bucket 42: 70%\n bucket 41: 80%\n bucket 42: 80%\n bucket 41: 90%\n bucket 42: 90%\n bucket 42: 100%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 43: 20%\n bucket 44: 10%\n bucket 43: 30%\n bucket 44: 20%\n bucket 43: 40%\n bucket 43: 50%\n bucket 44: 30%\n bucket 43: 60%\n bucket 44: 40%\n bucket 43: 70%\n bucket 44: 50%\n bucket 43: 80%\n bucket 44: 60%\n bucket 43: 90%\n bucket 44: 70%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n bucket 44: 80%\n (Using difference cover)\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n Entering block accumulator loop for bucket 46:\n bucket 45: 30%\n bucket 46: 10%\n bucket 45: 40%\n bucket 46: 20%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 46: 40%\n bucket 45: 70%\n bucket 46: 50%\n bucket 45: 80%\n bucket 46: 60%\n bucket 45: 90%\n bucket 46: 70%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n bucket 47: 70%\n Calculating Z arrays for bucket 48\n bucket 47: 80%\n bucket 47: 90%\n Entering block accumulator loop for bucket 48:\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n bucket 49: 30%\n Calculating Z arrays for bucket 50\n bucket 49: 40%\n bucket 49: 50%\n Entering block accumulator loop for bucket 50:\n bucket 49: 60%\n bucket 50: 10%\n bucket 49: 70%\n bucket 50: 20%\n bucket 49: 80%\n bucket 50: 30%\n bucket 49: 90%\n bucket 50: 40%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n Entering block accumulator loop for bucket 52:\n bucket 51: 20%\n bucket 52: 10%\n bucket 51: 30%\n bucket 52: 20%\n bucket 51: 40%\n bucket 52: 30%\n bucket 51: 50%\n bucket 52: 40%\n bucket 51: 60%\n bucket 52: 50%\n bucket 51: 70%\n bucket 51: 80%\n bucket 52: 60%\n bucket 51: 90%\n bucket 52: 70%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 53:\n Entering block accumulator loop for bucket 54:\n bucket 53: 10%\n bucket 53: 20%\n bucket 54: 10%\n bucket 53: 30%\n bucket 54: 20%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 54: 30%\n bucket 53: 70%\n bucket 54: 40%\n bucket 54: 50%\n bucket 53: 80%\n bucket 54: 60%\n bucket 53: 90%\n bucket 54: 70%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n bucket 54: 80%\n (Using difference cover)\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n bucket 55: 10%\n Calculating Z arrays for bucket 56\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n Entering block accumulator loop for bucket 56:\n bucket 55: 50%\n bucket 56: 10%\n bucket 55: 60%\n bucket 56: 20%\n bucket 55: 70%\n bucket 56: 30%\n bucket 55: 80%\n bucket 56: 40%\n bucket 55: 90%\n bucket 56: 50%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n bucket 58: 30%\n bucket 58: 40%\n Entering block accumulator loop for bucket 59:\n bucket 58: 50%\n bucket 58: 60%\n bucket 59: 10%\n bucket 58: 70%\n bucket 58: 80%\n bucket 59: 20%\n bucket 58: 90%\n bucket 59: 30%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n Reserving size (126) for bucket 3\nGetting block 5 of 60\n Reserving size (126) for bucket 5\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 5\n bucket 2: 10%\n bucket 1: 10%\n bucket 2: 20%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 5:\n Entering block accumulator loop for bucket 3:\n bucket 1: 20%\n bucket 2: 30%\n bucket 5: 10%\n bucket 2: 40%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 5: 20%\n bucket 2: 50%\n Entering block accumulator loop for bucket 4:\nGetting block 6 of 60\n bucket 2: 60%\n bucket 3: 10%\n bucket 1: 30%\n bucket 2: 70%\n Reserving size (126) for bucket 6\n bucket 4: 10%\n bucket 5: 30%\n bucket 1: 40%\n bucket 3: 20%\n Calculating Z arrays for bucket 7\n bucket 2: 80%\n Calculating Z arrays for bucket 6\n bucket 1: 50%\nGetting block 8 of 60\n Entering block accumulator loop for bucket 6:\n bucket 4: 20%\n Reserving size (126) for bucket 8\n bucket 2: 90%\n bucket 5: 40%\n bucket 6: 10%\n bucket 4: 30%\n bucket 2: 100%\n bucket 3: 30%\n bucket 5: 50%\n bucket 6: 20%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 1: 60%\n bucket 4: 40%\n bucket 3: 40%\n bucket 5: 60%\n Entering block accumulator loop for bucket 7:\n bucket 6: 30%\n Calculating Z arrays for bucket 8\n bucket 4: 50%\n bucket 5: 70%\n bucket 1: 70%\n bucket 6: 40%\n bucket 4: 60%\n bucket 5: 80%\n bucket 6: 50%\n bucket 3: 50%\n Entering block accumulator loop for bucket 8:\n bucket 1: 80%\n bucket 4: 70%\n bucket 5: 90%\n bucket 3: 60%\n bucket 7: 10%\n bucket 6: 60%\n bucket 1: 90%\n bucket 5: 100%\n bucket 4: 80%\n bucket 6: 70%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 10%\n bucket 1: 100%\n bucket 3: 70%\n bucket 7: 20%\n bucket 6: 80%\n bucket 4: 90%\n Sorting block of length 42 for bucket 1\n bucket 6: 90%\n (Using difference cover)\n bucket 3: 80%\n bucket 7: 30%\n bucket 8: 20%\n bucket 6: 100%\n bucket 3: 90%\n bucket 4: 100%\n bucket 7: 40%\n bucket 8: 30%\n bucket 3: 100%\n bucket 7: 50%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block of length 90 for bucket 6\n Sorting block time: 00:00:00\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n bucket 7: 60%\nReturning block of 85 for bucket 2\n (Using difference cover)\n bucket 8: 40%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 8: 50%\n bucket 7: 100%\n Sorting block of length 75 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 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\n Reserving size (126) for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 10:\n Entering block accumulator loop for bucket 9:\n bucket 10: 10%\n bucket 10: 20%\n bucket 9: 10%\n bucket 10: 30%\n bucket 9: 20%\n bucket 10: 40%\n bucket 9: 30%\n bucket 10: 50%\n bucket 9: 40%\n bucket 10: 60%\n bucket 9: 50%\n bucket 10: 70%\n bucket 9: 60%\n bucket 10: 80%\n bucket 9: 70%\n bucket 10: 90%\n bucket 9: 80%\n bucket 10: 100%\n bucket 9: 90%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) 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 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n Entering block accumulator loop for bucket 13:\n bucket 12: 20%\n bucket 12: 30%\n bucket 13: 10%\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 12: 60%\n bucket 13: 30%\nGetting block 14 of 60\n bucket 12: 70%\n bucket 13: 40%\n Reserving size (126) for bucket 14\n bucket 12: 80%\n Calculating Z arrays for bucket 14\n bucket 13: 50%\n bucket 12: 90%\n bucket 13: 60%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Entering block accumulator loop for bucket 14:\n bucket 13: 70%\n bucket 13: 80%\n bucket 14: 10%\n bucket 13: 90%\n bucket 14: 20%\n bucket 13: 100%\n bucket 14: 30%\n Sorting block of length 85 for bucket 13\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 time: 00:00:00\n Sorting block of length 82 for bucket 14\n (Using difference cover)\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) 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%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 30%\n bucket 15: 40%\n Entering block accumulator loop for bucket 16:\n bucket 15: 50%\n bucket 16: 10%\n bucket 15: 60%\n bucket 16: 20%\n bucket 15: 70%\n bucket 16: 30%\n bucket 15: 80%\n bucket 16: 40%\n bucket 15: 90%\n bucket 16: 50%\n bucket 15: 100%\n bucket 16: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Entering block accumulator loop for bucket 17:\n Reserving size (126) 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 bucket 18: 70%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Entering block accumulator loop for bucket 19:\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n bucket 19: 20%\n Entering block accumulator loop for bucket 20:\n bucket 19: 30%\n bucket 20: 10%\n bucket 19: 40%\n bucket 20: 20%\n bucket 19: 50%\n bucket 19: 60%\n bucket 20: 30%\n bucket 19: 70%\n bucket 20: 40%\n bucket 19: 80%\n bucket 20: 50%\n bucket 19: 90%\n bucket 20: 60%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n Entering block accumulator loop for bucket 22:\n bucket 21: 20%\n bucket 22: 10%\n bucket 21: 30%\n bucket 22: 20%\n bucket 21: 40%\n bucket 22: 30%\n bucket 21: 50%\n bucket 22: 40%\n bucket 21: 60%\n bucket 22: 50%\n bucket 21: 70%\n bucket 22: 60%\n bucket 21: 80%\n bucket 22: 70%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n bucket 22: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\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 24: 10%\n bucket 24: 20%\n bucket 23: 10%\n bucket 24: 30%\n bucket 23: 20%\n bucket 24: 40%\n bucket 23: 30%\n bucket 24: 50%\n bucket 24: 60%\n bucket 23: 40%\n bucket 24: 70%\n bucket 23: 50%\n bucket 24: 80%\n bucket 24: 90%\n bucket 23: 60%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) 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 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n bucket 25: 50%\n bucket 25: 60%\n Entering block accumulator loop for bucket 26:\n bucket 25: 70%\n bucket 26: 10%\n bucket 25: 80%\n bucket 26: 20%\n bucket 25: 90%\n bucket 26: 30%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\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 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) 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%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 90%\n bucket 27: 100%\n Entering block accumulator loop for bucket 28:\n Sorting block of length 119 for bucket 27\n (Using difference cover)\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 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 29:\n bucket 30: 10%\n bucket 29: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 29: 20%\n bucket 30: 40%\n bucket 29: 30%\n bucket 30: 50%\n bucket 29: 40%\n bucket 30: 60%\n bucket 29: 50%\n bucket 30: 70%\n bucket 29: 60%\n bucket 30: 80%\n bucket 30: 90%\n bucket 29: 70%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 10%\n bucket 31: 20%\n Entering block accumulator loop for bucket 32:\n bucket 31: 30%\n bucket 32: 10%\n bucket 31: 40%\n bucket 32: 20%\n bucket 31: 50%\n bucket 32: 30%\n bucket 31: 60%\n bucket 32: 40%\n bucket 31: 70%\n bucket 32: 50%\n bucket 31: 80%\n bucket 32: 60%\n bucket 32: 70%\n bucket 31: 90%\n bucket 32: 80%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 34:\n Entering block accumulator loop for bucket 33:\n bucket 34: 10%\n bucket 33: 10%\n bucket 34: 20%\n bucket 33: 20%\n bucket 34: 30%\n bucket 33: 30%\n bucket 34: 40%\n bucket 33: 40%\n bucket 34: 50%\n bucket 33: 50%\n bucket 34: 60%\n bucket 33: 60%\n bucket 34: 70%\n bucket 33: 70%\n bucket 34: 80%\n bucket 33: 80%\n bucket 34: 90%\n bucket 33: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n bucket 35: 90%\n Calculating Z arrays for bucket 36\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 37:\n Entering block accumulator loop for bucket 38:\n bucket 37: 10%\n bucket 38: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 38: 20%\n bucket 37: 40%\n bucket 38: 30%\n bucket 37: 50%\n bucket 37: 60%\n bucket 38: 40%\n bucket 37: 70%\n bucket 38: 50%\n bucket 37: 80%\n bucket 37: 90%\n bucket 38: 60%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n Entering block accumulator loop for bucket 40:\n bucket 39: 20%\n bucket 40: 10%\n bucket 39: 30%\n bucket 40: 20%\n bucket 39: 40%\n bucket 40: 30%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n Sorting block time: 00:00:00\n bucket 40: 80%\nReturning block of 126 for bucket 39\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 60\n Entering block accumulator loop for bucket 41:\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 41: 10%\n Entering block accumulator loop for bucket 42:\n bucket 41: 20%\n bucket 42: 10%\n bucket 41: 30%\n bucket 42: 20%\n bucket 41: 40%\n bucket 42: 30%\n bucket 41: 50%\n bucket 42: 40%\n bucket 41: 60%\n bucket 42: 50%\n bucket 42: 60%\n bucket 41: 70%\n bucket 42: 70%\n bucket 41: 80%\n bucket 42: 80%\n bucket 41: 90%\n bucket 42: 90%\n bucket 42: 100%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 43: 20%\n bucket 44: 10%\n bucket 43: 30%\n bucket 44: 20%\n bucket 43: 40%\n bucket 43: 50%\n bucket 44: 30%\n bucket 43: 60%\n bucket 44: 40%\n bucket 43: 70%\n bucket 44: 50%\n bucket 43: 80%\n bucket 44: 60%\n bucket 43: 90%\n bucket 44: 70%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n bucket 44: 80%\n (Using difference cover)\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n Entering block accumulator loop for bucket 46:\n bucket 45: 30%\n bucket 46: 10%\n bucket 45: 40%\n bucket 46: 20%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 46: 40%\n bucket 45: 70%\n bucket 46: 50%\n bucket 45: 80%\n bucket 46: 60%\n bucket 45: 90%\n bucket 46: 70%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n bucket 47: 70%\n Calculating Z arrays for bucket 48\n bucket 47: 80%\n bucket 47: 90%\n Entering block accumulator loop for bucket 48:\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n bucket 49: 30%\n Calculating Z arrays for bucket 50\n bucket 49: 40%\n bucket 49: 50%\n Entering block accumulator loop for bucket 50:\n bucket 49: 60%\n bucket 50: 10%\n bucket 49: 70%\n bucket 50: 20%\n bucket 49: 80%\n bucket 50: 30%\n bucket 49: 90%\n bucket 50: 40%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n Entering block accumulator loop for bucket 52:\n bucket 51: 20%\n bucket 52: 10%\n bucket 51: 30%\n bucket 52: 20%\n bucket 51: 40%\n bucket 52: 30%\n bucket 51: 50%\n bucket 52: 40%\n bucket 51: 60%\n bucket 52: 50%\n bucket 51: 70%\n bucket 51: 80%\n bucket 52: 60%\n bucket 51: 90%\n bucket 52: 70%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 53:\n Entering block accumulator loop for bucket 54:\n bucket 53: 10%\n bucket 53: 20%\n bucket 54: 10%\n bucket 53: 30%\n bucket 54: 20%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 54: 30%\n bucket 53: 70%\n bucket 54: 40%\n bucket 54: 50%\n bucket 53: 80%\n bucket 54: 60%\n bucket 53: 90%\n bucket 54: 70%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n bucket 54: 80%\n (Using difference cover)\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n bucket 55: 10%\n Calculating Z arrays for bucket 56\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n Entering block accumulator loop for bucket 56:\n bucket 55: 50%\n bucket 56: 10%\n bucket 55: 60%\n bucket 56: 20%\n bucket 55: 70%\n bucket 56: 30%\n bucket 55: 80%\n bucket 56: 40%\n bucket 55: 90%\n bucket 56: 50%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n bucket 58: 30%\n bucket 58: 40%\n Entering block accumulator loop for bucket 59:\n bucket 58: 50%\n bucket 58: 60%\n bucket 59: 10%\n bucket 58: 70%\n bucket 58: 80%\n bucket 59: 20%\n bucket 58: 90%\n bucket 59: 30%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:36:01", "plugin": "core", "name": "end_epoch", "raw_value": "1736861761.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:36:01", "plugin": "core", "name": "start_epoch", "raw_value": "1736861761.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 16.982489585876465, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"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": 30.997881174087524, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "55c451aaa605f510"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "b04c966e5b50eb78"}, "library|type": "single", "adv|output_options|unaligned_file": true, "adv|output_options|output_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "35f84111fd7775c6", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:36:59.686272", "create_time": "2025-01-14T13:36:47.105370", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-98njb", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/b/0/3/dataset_b039ad29-d6aa-4489-a1b0-c9ae913866fc.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/a/d/d/dataset_addc01a4-3e98-495e-a0a8-7d3619033488.dat' input_f.fasta && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -f -U 'input_f.fasta' --un '/galaxy/server/database/objects/8/c/6/dataset_8c606e07-7c70-4f49-a21b-31a26f97b34a.dat' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/e/c/a/dataset_ecad4d71-37de-42d6-bbeb-c0dd0ed30b1b.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\": 214, \"src\": \"hda\"}]}, \"rna_strandness\": \"\", \"type\": \"single\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 213, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "55c451aaa605f510", "src": "hda", "uuid": "b039ad29-d6aa-4489-a1b0-c9ae913866fc"}, "library|input_1": {"id": "b04c966e5b50eb78", "src": "hda", "uuid": "addc01a4-3e98-495e-a0a8-7d3619033488"}}, "outputs": {"output_alignments": {"id": "131dc35c72ea16a3", "src": "hda", "uuid": "ecad4d71-37de-42d6-bbeb-c0dd0ed30b1b"}, "output_unaligned_reads_l": {"id": "c30773bab04efc03", "src": "hda", "uuid": "8c606e07-7c70-4f49-a21b-31a26f97b34a"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n bucket 2: 10%\n bucket 1: 40%\n bucket 1: 50%\n bucket 2: 20%\n bucket 1: 60%\nGetting block 3 of 60\n bucket 1: 70%\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\n bucket 1: 80%\n bucket 1: 90%\n bucket 1: 100%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Entering block accumulator loop for bucket 3:\n bucket 3: 10%\nGetting block 4 of 60\n bucket 3: 20%\n bucket 2: 30%\n bucket 3: 30%\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 4\n bucket 3: 40%\n bucket 2: 40%\n bucket 3: 50%\n Entering block accumulator loop for bucket 4:\n bucket 2: 50%\n bucket 3: 60%\n bucket 4: 10%\n bucket 2: 60%\n bucket 3: 70%\n bucket 2: 70%\n bucket 4: 20%\n bucket 3: 80%\n bucket 2: 80%\n bucket 3: 90%\n bucket 4: 30%\n Sorting block time: 00:00:00\nGetting block 5 of 60\nReturning block of 43 for bucket 1\n bucket 3: 100%\n Reserving size (126) for bucket 5\n bucket 4: 40%\n bucket 2: 90%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 4: 50%\n bucket 2: 100%\n Calculating Z arrays for bucket 5\n bucket 4: 60%\n Sorting block of length 84 for bucket 2\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 68 for bucket 4\n (Using difference cover)\nGetting block 6 of 60\n Reserving size (126) 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 bucket 5: 60%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 5: 70%\n Calculating Z arrays for bucket 7\n bucket 5: 80%\n bucket 5: 90%\n Entering block accumulator loop for bucket 7:\n Calculating Z arrays for bucket 6\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n Entering block accumulator loop for bucket 6:\n bucket 7: 10%\n bucket 7: 20%\n bucket 6: 10%\n bucket 7: 30%\n bucket 7: 40%\n bucket 6: 20%\n bucket 7: 50%\n bucket 7: 60%\n bucket 6: 30%\n bucket 7: 70%\n bucket 6: 40%\n bucket 7: 80%\n bucket 6: 50%\n bucket 7: 90%\n bucket 6: 60%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Calculating Z arrays for bucket 8\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\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 Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) 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 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 20%\n bucket 10: 30%\n Entering block accumulator loop for bucket 11:\n bucket 10: 40%\n bucket 11: 10%\n bucket 10: 50%\n bucket 11: 20%\n bucket 10: 60%\n bucket 10: 70%\n bucket 11: 30%\n bucket 10: 80%\n bucket 11: 40%\n bucket 10: 90%\n bucket 11: 50%\n bucket 10: 100%\n bucket 11: 60%\n Sorting block of length 89 for bucket 10\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 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 13:\n bucket 12: 10%\n bucket 12: 20%\n bucket 13: 10%\n bucket 12: 30%\n bucket 13: 20%\n bucket 12: 40%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\n bucket 13: 40%\n bucket 12: 70%\n bucket 13: 50%\n bucket 12: 80%\n bucket 13: 60%\n bucket 12: 90%\n bucket 13: 70%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\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 Entering block accumulator loop for bucket 14:\n bucket 15: 50%\n bucket 15: 60%\n bucket 14: 10%\n bucket 15: 70%\n bucket 14: 20%\n bucket 15: 80%\n bucket 14: 30%\n bucket 15: 90%\n bucket 14: 40%\n bucket 15: 100%\n bucket 14: 50%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\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 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 16 of 60\n Reserving size (126) 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%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n Entering block accumulator loop for bucket 17:\n bucket 16: 60%\n bucket 16: 70%\n bucket 17: 10%\n bucket 16: 80%\n bucket 17: 20%\n bucket 16: 90%\n bucket 17: 30%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\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 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Entering block accumulator loop for bucket 18:\n Calculating Z arrays for bucket 19\n bucket 18: 10%\n bucket 18: 20%\n Entering block accumulator loop for bucket 19:\n bucket 18: 30%\n bucket 19: 10%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 19: 50%\n bucket 18: 80%\n bucket 19: 60%\n bucket 18: 90%\n bucket 19: 70%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 20\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\n Entering block accumulator loop for bucket 21:\n bucket 20: 10%\n bucket 21: 10%\n bucket 20: 20%\n bucket 21: 20%\n bucket 20: 30%\n bucket 21: 30%\n bucket 20: 40%\n bucket 21: 40%\n bucket 20: 50%\n bucket 21: 50%\n bucket 20: 60%\n bucket 21: 60%\n bucket 20: 70%\n bucket 21: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n Entering block accumulator loop for bucket 23:\n bucket 22: 10%\n bucket 23: 10%\n bucket 22: 20%\n bucket 23: 20%\n bucket 22: 30%\n bucket 23: 30%\n bucket 22: 40%\n bucket 23: 40%\n bucket 22: 50%\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 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\n Reserving size (126) 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%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 70%\n bucket 24: 80%\n Entering block accumulator loop for bucket 25:\n bucket 24: 90%\n bucket 25: 10%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\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 Sorting block time: 00:00:00\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 26: 10%\n bucket 27: 20%\n bucket 26: 20%\n bucket 27: 30%\n bucket 26: 30%\n bucket 27: 40%\n bucket 26: 40%\n bucket 27: 50%\n bucket 26: 50%\n bucket 27: 60%\n bucket 26: 60%\n bucket 27: 70%\n bucket 26: 70%\n bucket 27: 80%\n bucket 26: 80%\n bucket 27: 90%\n bucket 26: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) 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%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 60%\n bucket 28: 70%\n Entering block accumulator loop for bucket 29:\n bucket 28: 80%\n bucket 28: 90%\n bucket 29: 10%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\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 107 for bucket 28\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 31: 30%\n bucket 32: 10%\n bucket 31: 40%\n bucket 32: 20%\n bucket 31: 50%\n bucket 31: 60%\n bucket 32: 30%\n bucket 31: 70%\n bucket 32: 40%\n bucket 31: 80%\n bucket 32: 50%\n bucket 31: 90%\n bucket 31: 100%\n bucket 32: 60%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Entering block accumulator loop for bucket 33:\n Calculating Z arrays for bucket 34\n bucket 33: 10%\n bucket 33: 20%\n Entering block accumulator loop for bucket 34:\n bucket 33: 30%\n bucket 34: 10%\n bucket 33: 40%\n bucket 34: 20%\n bucket 33: 50%\n bucket 34: 30%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 34: 40%\n bucket 33: 90%\n bucket 34: 50%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\nGetting block 37 of 60\n bucket 36: 20%\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 30%\n bucket 36: 40%\n Entering block accumulator loop for bucket 37:\n bucket 36: 50%\n bucket 37: 10%\n bucket 36: 60%\n bucket 37: 20%\n bucket 36: 70%\n bucket 37: 30%\n bucket 36: 80%\n bucket 37: 40%\n bucket 36: 90%\n bucket 37: 50%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n bucket 37: 60%\n (Using difference cover)\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n bucket 38: 50%\n Calculating Z arrays for bucket 39\n bucket 38: 60%\n Entering block accumulator loop for bucket 39:\n bucket 38: 70%\n bucket 39: 10%\n bucket 39: 20%\n bucket 38: 80%\n bucket 39: 30%\n bucket 38: 90%\n bucket 39: 40%\n bucket 38: 100%\n bucket 39: 50%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\nGetting block 42 of 60\n Calculating Z arrays for bucket 41\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 42:\n bucket 41: 10%\n bucket 42: 10%\n bucket 41: 20%\n bucket 42: 20%\n bucket 41: 30%\n bucket 42: 30%\n bucket 41: 40%\n bucket 42: 40%\n bucket 41: 50%\n bucket 42: 50%\n bucket 41: 60%\n bucket 42: 60%\n bucket 41: 70%\n bucket 42: 70%\n bucket 41: 80%\n bucket 42: 80%\n bucket 41: 90%\n bucket 42: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Entering block accumulator loop for bucket 43:\n Calculating Z arrays for bucket 44\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 43: 20%\n bucket 44: 10%\n bucket 43: 30%\n bucket 44: 20%\n bucket 43: 40%\n bucket 44: 30%\n bucket 44: 40%\n bucket 43: 50%\n bucket 44: 50%\n bucket 43: 60%\n bucket 44: 60%\n bucket 43: 70%\n bucket 44: 70%\n bucket 43: 80%\n bucket 44: 80%\n bucket 43: 90%\n bucket 44: 90%\n bucket 43: 100%\n bucket 44: 100%\n Sorting block of length 121 for bucket 43\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\nGetting block 47 of 60\n bucket 46: 70%\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Entering block accumulator loop for bucket 48:\n Calculating Z arrays for bucket 49\n bucket 48: 10%\n Entering block accumulator loop for bucket 49:\n bucket 48: 20%\n bucket 49: 10%\n bucket 48: 30%\n bucket 49: 20%\n bucket 48: 40%\n bucket 49: 30%\n bucket 48: 50%\n bucket 49: 40%\n bucket 48: 60%\n bucket 49: 50%\n bucket 48: 70%\n bucket 49: 60%\n bucket 48: 80%\n bucket 49: 70%\n bucket 48: 90%\n bucket 49: 80%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n bucket 49: 90%\n (Using difference cover)\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Entering block accumulator loop for bucket 51:\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n Entering block accumulator loop for bucket 52:\n bucket 51: 20%\n bucket 52: 10%\n bucket 51: 30%\n bucket 52: 20%\n bucket 51: 40%\n bucket 51: 50%\n bucket 52: 30%\n bucket 51: 60%\n bucket 52: 40%\n bucket 51: 70%\n bucket 52: 50%\n bucket 51: 80%\n bucket 52: 60%\n bucket 51: 90%\n bucket 51: 100%\n bucket 52: 70%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 54\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 54:\n bucket 55: 10%\n bucket 54: 10%\n bucket 55: 20%\n bucket 54: 20%\n bucket 55: 30%\n bucket 54: 30%\n bucket 55: 40%\n bucket 54: 40%\n bucket 55: 50%\n bucket 54: 50%\n bucket 55: 60%\n bucket 54: 60%\n bucket 55: 70%\n bucket 54: 70%\n bucket 55: 80%\n bucket 54: 80%\n bucket 55: 90%\n bucket 54: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n Entering block accumulator loop for bucket 57:\n bucket 56: 70%\n bucket 56: 80%\n bucket 57: 10%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 58:\n Entering block accumulator loop for bucket 59:\n bucket 58: 10%\n bucket 59: 10%\n bucket 58: 20%\n bucket 59: 20%\n bucket 58: 30%\n bucket 59: 30%\n bucket 58: 40%\n bucket 59: 40%\n bucket 58: 50%\n bucket 59: 50%\n bucket 58: 60%\n bucket 59: 60%\n bucket 58: 70%\n bucket 59: 70%\n bucket 58: 80%\n bucket 59: 80%\n bucket 58: 90%\n bucket 59: 90%\n bucket 58: 100%\n bucket 59: 100%\n Sorting block of length 113 for bucket 58\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n bucket 2: 10%\n bucket 1: 40%\n bucket 1: 50%\n bucket 2: 20%\n bucket 1: 60%\nGetting block 3 of 60\n bucket 1: 70%\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\n bucket 1: 80%\n bucket 1: 90%\n bucket 1: 100%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Entering block accumulator loop for bucket 3:\n bucket 3: 10%\nGetting block 4 of 60\n bucket 3: 20%\n bucket 2: 30%\n bucket 3: 30%\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 4\n bucket 3: 40%\n bucket 2: 40%\n bucket 3: 50%\n Entering block accumulator loop for bucket 4:\n bucket 2: 50%\n bucket 3: 60%\n bucket 4: 10%\n bucket 2: 60%\n bucket 3: 70%\n bucket 2: 70%\n bucket 4: 20%\n bucket 3: 80%\n bucket 2: 80%\n bucket 3: 90%\n bucket 4: 30%\n Sorting block time: 00:00:00\nGetting block 5 of 60\nReturning block of 43 for bucket 1\n bucket 3: 100%\n Reserving size (126) for bucket 5\n bucket 4: 40%\n bucket 2: 90%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 4: 50%\n bucket 2: 100%\n Calculating Z arrays for bucket 5\n bucket 4: 60%\n Sorting block of length 84 for bucket 2\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 68 for bucket 4\n (Using difference cover)\nGetting block 6 of 60\n Reserving size (126) 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 bucket 5: 60%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 5: 70%\n Calculating Z arrays for bucket 7\n bucket 5: 80%\n bucket 5: 90%\n Entering block accumulator loop for bucket 7:\n Calculating Z arrays for bucket 6\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n Entering block accumulator loop for bucket 6:\n bucket 7: 10%\n bucket 7: 20%\n bucket 6: 10%\n bucket 7: 30%\n bucket 7: 40%\n bucket 6: 20%\n bucket 7: 50%\n bucket 7: 60%\n bucket 6: 30%\n bucket 7: 70%\n bucket 6: 40%\n bucket 7: 80%\n bucket 6: 50%\n bucket 7: 90%\n bucket 6: 60%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 6: 70%\n bucket 6: 80%\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Calculating Z arrays for bucket 8\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\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 Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) 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 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 20%\n bucket 10: 30%\n Entering block accumulator loop for bucket 11:\n bucket 10: 40%\n bucket 11: 10%\n bucket 10: 50%\n bucket 11: 20%\n bucket 10: 60%\n bucket 10: 70%\n bucket 11: 30%\n bucket 10: 80%\n bucket 11: 40%\n bucket 10: 90%\n bucket 11: 50%\n bucket 10: 100%\n bucket 11: 60%\n Sorting block of length 89 for bucket 10\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 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 13:\n bucket 12: 10%\n bucket 12: 20%\n bucket 13: 10%\n bucket 12: 30%\n bucket 13: 20%\n bucket 12: 40%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\n bucket 13: 40%\n bucket 12: 70%\n bucket 13: 50%\n bucket 12: 80%\n bucket 13: 60%\n bucket 12: 90%\n bucket 13: 70%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\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 Entering block accumulator loop for bucket 14:\n bucket 15: 50%\n bucket 15: 60%\n bucket 14: 10%\n bucket 15: 70%\n bucket 14: 20%\n bucket 15: 80%\n bucket 14: 30%\n bucket 15: 90%\n bucket 14: 40%\n bucket 15: 100%\n bucket 14: 50%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\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 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 16 of 60\n Reserving size (126) 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%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n Entering block accumulator loop for bucket 17:\n bucket 16: 60%\n bucket 16: 70%\n bucket 17: 10%\n bucket 16: 80%\n bucket 17: 20%\n bucket 16: 90%\n bucket 17: 30%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\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 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Entering block accumulator loop for bucket 18:\n Calculating Z arrays for bucket 19\n bucket 18: 10%\n bucket 18: 20%\n Entering block accumulator loop for bucket 19:\n bucket 18: 30%\n bucket 19: 10%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 19: 50%\n bucket 18: 80%\n bucket 19: 60%\n bucket 18: 90%\n bucket 19: 70%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 20\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\n Entering block accumulator loop for bucket 21:\n bucket 20: 10%\n bucket 21: 10%\n bucket 20: 20%\n bucket 21: 20%\n bucket 20: 30%\n bucket 21: 30%\n bucket 20: 40%\n bucket 21: 40%\n bucket 20: 50%\n bucket 21: 50%\n bucket 20: 60%\n bucket 21: 60%\n bucket 20: 70%\n bucket 21: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n Entering block accumulator loop for bucket 23:\n bucket 22: 10%\n bucket 23: 10%\n bucket 22: 20%\n bucket 23: 20%\n bucket 22: 30%\n bucket 23: 30%\n bucket 22: 40%\n bucket 23: 40%\n bucket 22: 50%\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 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\n Reserving size (126) 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%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 70%\n bucket 24: 80%\n Entering block accumulator loop for bucket 25:\n bucket 24: 90%\n bucket 25: 10%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\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 Sorting block time: 00:00:00\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 26: 10%\n bucket 27: 20%\n bucket 26: 20%\n bucket 27: 30%\n bucket 26: 30%\n bucket 27: 40%\n bucket 26: 40%\n bucket 27: 50%\n bucket 26: 50%\n bucket 27: 60%\n bucket 26: 60%\n bucket 27: 70%\n bucket 26: 70%\n bucket 27: 80%\n bucket 26: 80%\n bucket 27: 90%\n bucket 26: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) 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%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 60%\n bucket 28: 70%\n Entering block accumulator loop for bucket 29:\n bucket 28: 80%\n bucket 28: 90%\n bucket 29: 10%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\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 107 for bucket 28\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 31: 30%\n bucket 32: 10%\n bucket 31: 40%\n bucket 32: 20%\n bucket 31: 50%\n bucket 31: 60%\n bucket 32: 30%\n bucket 31: 70%\n bucket 32: 40%\n bucket 31: 80%\n bucket 32: 50%\n bucket 31: 90%\n bucket 31: 100%\n bucket 32: 60%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Entering block accumulator loop for bucket 33:\n Calculating Z arrays for bucket 34\n bucket 33: 10%\n bucket 33: 20%\n Entering block accumulator loop for bucket 34:\n bucket 33: 30%\n bucket 34: 10%\n bucket 33: 40%\n bucket 34: 20%\n bucket 33: 50%\n bucket 34: 30%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 34: 40%\n bucket 33: 90%\n bucket 34: 50%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\nGetting block 37 of 60\n bucket 36: 20%\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 30%\n bucket 36: 40%\n Entering block accumulator loop for bucket 37:\n bucket 36: 50%\n bucket 37: 10%\n bucket 36: 60%\n bucket 37: 20%\n bucket 36: 70%\n bucket 37: 30%\n bucket 36: 80%\n bucket 37: 40%\n bucket 36: 90%\n bucket 37: 50%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n bucket 37: 60%\n (Using difference cover)\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n bucket 38: 50%\n Calculating Z arrays for bucket 39\n bucket 38: 60%\n Entering block accumulator loop for bucket 39:\n bucket 38: 70%\n bucket 39: 10%\n bucket 39: 20%\n bucket 38: 80%\n bucket 39: 30%\n bucket 38: 90%\n bucket 39: 40%\n bucket 38: 100%\n bucket 39: 50%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\nGetting block 42 of 60\n Calculating Z arrays for bucket 41\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 42:\n bucket 41: 10%\n bucket 42: 10%\n bucket 41: 20%\n bucket 42: 20%\n bucket 41: 30%\n bucket 42: 30%\n bucket 41: 40%\n bucket 42: 40%\n bucket 41: 50%\n bucket 42: 50%\n bucket 41: 60%\n bucket 42: 60%\n bucket 41: 70%\n bucket 42: 70%\n bucket 41: 80%\n bucket 42: 80%\n bucket 41: 90%\n bucket 42: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Entering block accumulator loop for bucket 43:\n Calculating Z arrays for bucket 44\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 43: 20%\n bucket 44: 10%\n bucket 43: 30%\n bucket 44: 20%\n bucket 43: 40%\n bucket 44: 30%\n bucket 44: 40%\n bucket 43: 50%\n bucket 44: 50%\n bucket 43: 60%\n bucket 44: 60%\n bucket 43: 70%\n bucket 44: 70%\n bucket 43: 80%\n bucket 44: 80%\n bucket 43: 90%\n bucket 44: 90%\n bucket 43: 100%\n bucket 44: 100%\n Sorting block of length 121 for bucket 43\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\nGetting block 47 of 60\n bucket 46: 70%\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Entering block accumulator loop for bucket 48:\n Calculating Z arrays for bucket 49\n bucket 48: 10%\n Entering block accumulator loop for bucket 49:\n bucket 48: 20%\n bucket 49: 10%\n bucket 48: 30%\n bucket 49: 20%\n bucket 48: 40%\n bucket 49: 30%\n bucket 48: 50%\n bucket 49: 40%\n bucket 48: 60%\n bucket 49: 50%\n bucket 48: 70%\n bucket 49: 60%\n bucket 48: 80%\n bucket 49: 70%\n bucket 48: 90%\n bucket 49: 80%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n bucket 49: 90%\n (Using difference cover)\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Entering block accumulator loop for bucket 51:\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n Entering block accumulator loop for bucket 52:\n bucket 51: 20%\n bucket 52: 10%\n bucket 51: 30%\n bucket 52: 20%\n bucket 51: 40%\n bucket 51: 50%\n bucket 52: 30%\n bucket 51: 60%\n bucket 52: 40%\n bucket 51: 70%\n bucket 52: 50%\n bucket 51: 80%\n bucket 52: 60%\n bucket 51: 90%\n bucket 51: 100%\n bucket 52: 70%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 54\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 54:\n bucket 55: 10%\n bucket 54: 10%\n bucket 55: 20%\n bucket 54: 20%\n bucket 55: 30%\n bucket 54: 30%\n bucket 55: 40%\n bucket 54: 40%\n bucket 55: 50%\n bucket 54: 50%\n bucket 55: 60%\n bucket 54: 60%\n bucket 55: 70%\n bucket 54: 70%\n bucket 55: 80%\n bucket 54: 80%\n bucket 55: 90%\n bucket 54: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n Entering block accumulator loop for bucket 57:\n bucket 56: 70%\n bucket 56: 80%\n bucket 57: 10%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 58:\n Entering block accumulator loop for bucket 59:\n bucket 58: 10%\n bucket 59: 10%\n bucket 58: 20%\n bucket 59: 20%\n bucket 58: 30%\n bucket 59: 30%\n bucket 58: 40%\n bucket 59: 40%\n bucket 58: 50%\n bucket 59: 50%\n bucket 58: 60%\n bucket 59: 60%\n bucket 58: 70%\n bucket 59: 70%\n bucket 58: 80%\n bucket 59: 80%\n bucket 58: 90%\n bucket 59: 90%\n bucket 58: 100%\n bucket 59: 100%\n Sorting block of length 113 for bucket 58\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:36:49", "plugin": "core", "name": "end_epoch", "raw_value": "1736861809.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:36:49", "plugin": "core", "name": "start_epoch", "raw_value": "1736861809.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 29.51522159576416, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "56257b3c50d61efb"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "1d9da8490e8cad74"}, "library|input_2": {"src": "hda", "id": "1d9da8490e8cad74"}, "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": "3fdac4cc9c09299e", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:37:28.635330", "create_time": "2025-01-14T13:37:16.694438", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-54lgd", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/c/0/2/dataset_c0265e29-50d4-45f7-82ba-c3971766eafb.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/7/e/4/dataset_7e43c41c-459c-4369-8455-873397fe46ba.dat' input_f.fasta && ln -f -s '/galaxy/server/database/objects/7/e/4/dataset_7e43c41c-459c-4369-8455-873397fe46ba.dat' input_r.fasta && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -f -1 'input_f.fasta' -2 'input_r.fasta' --un-conc '/galaxy/server/database/objects/f/1/d/dataset_f1dca442-22fb-48a7-af7b-f9da57f2a543.dat' --al-conc '/galaxy/server/database/objects/3/0/b/dataset_30b8e49c-2d58-48e4-97fa-df5eeffd6db6.dat' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/7/9/d/dataset_79d00317-4e44-4a23-83b3-ef67b74d5365.dat' && mv '/galaxy/server/database/objects/f/1/d/dataset_f1dca442-22fb-48a7-af7b-f9da57f2a543.1.dat' '/galaxy/server/database/objects/f/1/d/dataset_f1dca442-22fb-48a7-af7b-f9da57f2a543.dat' && mv '/galaxy/server/database/objects/f/1/d/dataset_f1dca442-22fb-48a7-af7b-f9da57f2a543.2.dat' '/galaxy/server/database/objects/c/9/7/dataset_c97ab7bc-7c0c-475c-bd49-f9c8a473a99f.dat' && mv '/galaxy/server/database/objects/3/0/b/dataset_30b8e49c-2d58-48e4-97fa-df5eeffd6db6.1.dat' '/galaxy/server/database/objects/3/0/b/dataset_30b8e49c-2d58-48e4-97fa-df5eeffd6db6.dat' && mv '/galaxy/server/database/objects/3/0/b/dataset_30b8e49c-2d58-48e4-97fa-df5eeffd6db6.2.dat' '/galaxy/server/database/objects/d/8/9/dataset_d8975e41-82ab-471d-b5f9-9f1a8018b9bd.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\": 218, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 218, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 217, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "56257b3c50d61efb", "src": "hda", "uuid": "c0265e29-50d4-45f7-82ba-c3971766eafb"}, "library|input_1": {"id": "1d9da8490e8cad74", "src": "hda", "uuid": "7e43c41c-459c-4369-8455-873397fe46ba"}, "library|input_2": {"id": "1d9da8490e8cad74", "src": "hda", "uuid": "7e43c41c-459c-4369-8455-873397fe46ba"}}, "outputs": {"output_alignments": {"id": "97991e5e0b89d9b1", "src": "hda", "uuid": "79d00317-4e44-4a23-83b3-ef67b74d5365"}, "output_unaligned_reads_l": {"id": "b33f15e654ef4256", "src": "hda", "uuid": "f1dca442-22fb-48a7-af7b-f9da57f2a543"}, "output_aligned_reads_l": {"id": "e3cc38847b487d29", "src": "hda", "uuid": "30b8e49c-2d58-48e4-97fa-df5eeffd6db6"}, "output_unaligned_reads_r": {"id": "c2201f7a79c03f0b", "src": "hda", "uuid": "c97ab7bc-7c0c-475c-bd49-f9c8a473a99f"}, "output_aligned_reads_r": {"id": "f451d5d464b20ad3", "src": "hda", "uuid": "d8975e41-82ab-471d-b5f9-9f1a8018b9bd"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\nGetting block 3 of 60\nGetting block 4 of 60\n bucket 1: 10%\n Reserving size (126) for bucket 3\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 2:\n bucket 1: 20%\n Entering block accumulator loop for bucket 3:\nGetting block 5 of 60\n bucket 2: 10%\n Reserving size (126) for bucket 5\n bucket 3: 10%\n Calculating Z arrays for bucket 5\n bucket 2: 20%\n Entering block accumulator loop for bucket 4:\nGetting block 7 of 60\n Entering block accumulator loop for bucket 5:\n bucket 2: 30%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 4: 10%\n bucket 3: 20%\n Reserving size (126) for bucket 7\n Calculating Z arrays for bucket 6\n bucket 4: 20%\n Calculating Z arrays for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 1: 30%\n bucket 2: 40%\n Entering block accumulator loop for bucket 6:\n bucket 3: 30%\n Calculating Z arrays for bucket 8\n bucket 2: 50%\n bucket 5: 10%\n bucket 4: 30%\n Entering block accumulator loop for bucket 7:\n bucket 2: 60%\n bucket 4: 40%\n bucket 3: 40%\n bucket 6: 10%\n Entering block accumulator loop for bucket 8:\n bucket 4: 50%\n bucket 2: 70%\n bucket 6: 20%\n bucket 3: 50%\n bucket 7: 10%\n bucket 2: 80%\n bucket 4: 60%\n bucket 6: 30%\n bucket 5: 20%\n bucket 4: 70%\n bucket 2: 90%\n bucket 3: 60%\n bucket 1: 40%\n bucket 4: 80%\n bucket 6: 40%\n bucket 7: 20%\n bucket 3: 70%\n bucket 4: 90%\n bucket 8: 10%\n bucket 6: 50%\n bucket 7: 30%\n bucket 2: 100%\n bucket 1: 50%\n Sorting block of length 84 for bucket 2\n bucket 6: 60%\n (Using difference cover)\n bucket 8: 20%\n bucket 7: 40%\n bucket 6: 70%\n bucket 3: 80%\n bucket 1: 60%\n bucket 4: 100%\n bucket 7: 50%\n bucket 3: 90%\n bucket 6: 80%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 5: 30%\n bucket 6: 90%\n bucket 3: 100%\n bucket 7: 60%\n Sorting block of length 106 for bucket 3\n bucket 7: 70%\n (Using difference cover)\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 30%\n bucket 7: 80%\n bucket 5: 40%\n bucket 1: 70%\n bucket 7: 90%\n bucket 8: 40%\n bucket 5: 50%\n bucket 7: 100%\n bucket 1: 80%\n bucket 8: 50%\n bucket 5: 60%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 1: 90%\n bucket 8: 60%\n bucket 5: 70%\n bucket 1: 100%\n bucket 5: 80%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 8: 70%\n bucket 5: 90%\n bucket 8: 80%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\nGetting block 10 of 60\n bucket 9: 10%\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 20%\n bucket 9: 30%\n Entering block accumulator loop for bucket 10:\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 124 for bucket 9\n bucket 10: 70%\n (Using difference cover)\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Entering block accumulator loop for bucket 11:\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 10%\n bucket 11: 20%\n Entering block accumulator loop for bucket 12:\n bucket 11: 30%\n bucket 12: 10%\n bucket 11: 40%\n bucket 12: 20%\n bucket 11: 50%\n bucket 12: 30%\n bucket 11: 60%\n bucket 12: 40%\n bucket 11: 70%\n bucket 12: 50%\n bucket 11: 80%\n bucket 12: 60%\n bucket 11: 90%\n bucket 12: 70%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) 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 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) 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%\nGetting block 15 of 60\n bucket 14: 70%\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 17 of 60\n bucket 14: 80%\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 15:\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 14: 90%\n bucket 15: 10%\n bucket 14: 100%\n Entering block accumulator loop for bucket 17:\n bucket 15: 20%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 30%\n Entering block accumulator loop for bucket 16:\n bucket 15: 40%\n bucket 17: 10%\n bucket 15: 50%\n bucket 16: 10%\n bucket 15: 60%\n bucket 17: 20%\n bucket 15: 70%\n bucket 16: 20%\n bucket 15: 80%\n bucket 17: 30%\n bucket 15: 90%\n bucket 16: 30%\n bucket 17: 40%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 40%\n bucket 17: 50%\n bucket 16: 50%\n bucket 17: 60%\n bucket 16: 60%\n bucket 17: 70%\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n bucket 16: 70%\n bucket 17: 80%\n bucket 16: 80%\n bucket 17: 90%\n bucket 16: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 18:\n Entering block accumulator loop for bucket 19:\n bucket 18: 10%\n bucket 19: 10%\n bucket 18: 20%\n bucket 19: 20%\n bucket 18: 30%\n bucket 19: 30%\n bucket 18: 40%\n bucket 19: 40%\n bucket 19: 50%\n bucket 18: 50%\n bucket 19: 60%\n bucket 18: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 18: 70%\n bucket 19: 90%\n bucket 18: 80%\n bucket 18: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) 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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\nGetting block 22 of 60\n bucket 21: 10%\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 20%\n Entering block accumulator loop for bucket 22:\n bucket 21: 30%\n bucket 22: 10%\n bucket 21: 40%\n bucket 22: 20%\n bucket 21: 50%\n bucket 22: 30%\n bucket 21: 60%\n bucket 21: 70%\n bucket 22: 40%\n bucket 21: 80%\n bucket 22: 50%\n bucket 21: 90%\n bucket 22: 60%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n bucket 22: 70%\n bucket 22: 80%\n (Using difference cover)\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Entering block accumulator loop for bucket 23:\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 24: 10%\n bucket 23: 30%\n bucket 24: 20%\n bucket 23: 40%\n bucket 24: 30%\n bucket 23: 50%\n bucket 24: 40%\n bucket 23: 60%\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) 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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\nGetting block 27 of 60\n Reserving size (126) for bucket 26\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 26\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 26: 10%\n bucket 27: 20%\n bucket 26: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 26: 30%\n bucket 27: 50%\n bucket 26: 40%\n bucket 27: 60%\n bucket 27: 70%\n bucket 26: 50%\n bucket 27: 80%\n bucket 26: 60%\n bucket 27: 90%\n bucket 27: 100%\n bucket 26: 70%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\nGetting block 29 of 60\n bucket 28: 20%\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 30%\n bucket 28: 40%\n Entering block accumulator loop for bucket 29:\n bucket 28: 50%\n bucket 29: 10%\n bucket 28: 60%\n bucket 29: 20%\n bucket 28: 70%\n bucket 29: 30%\n bucket 28: 80%\n bucket 29: 40%\n bucket 28: 90%\n bucket 29: 50%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n Sorting block time: 00:00:00\n bucket 32: 30%\nReturning block of 111 for bucket 31\n bucket 32: 40%\n bucket 32: 50%\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\nGetting block 34 of 60\n bucket 33: 50%\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n Entering block accumulator loop for bucket 34:\n bucket 33: 90%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n bucket 33: 100%\n bucket 34: 10%\n Calculating Z arrays for bucket 35\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 20%\n Entering block accumulator loop for bucket 35:\n bucket 34: 30%\n bucket 35: 10%\n bucket 34: 40%\n bucket 35: 20%\n bucket 34: 50%\n bucket 35: 30%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n Sorting block time: 00:00:00\n bucket 35: 40%\nReturning block of 45 for bucket 33\n bucket 34: 90%\n bucket 35: 50%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n bucket 35: 60%\n (Using difference cover)\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n Entering block accumulator loop for bucket 39:\n bucket 38: 90%\n bucket 38: 100%\n bucket 39: 10%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\nGetting block 42 of 60\n bucket 41: 80%\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 41: 90%\n bucket 41: 100%\n Entering block accumulator loop for bucket 42:\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n bucket 43: 60%\n Entering block accumulator loop for bucket 44:\n bucket 43: 70%\n bucket 44: 10%\n bucket 43: 80%\n bucket 44: 20%\n bucket 43: 90%\n bucket 44: 30%\n bucket 43: 100%\n bucket 44: 40%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Entering block accumulator loop for bucket 45:\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n bucket 45: 20%\n Entering block accumulator loop for bucket 46:\n bucket 45: 30%\n bucket 45: 40%\n bucket 46: 10%\n bucket 45: 50%\n bucket 46: 20%\n bucket 45: 60%\n bucket 46: 30%\n bucket 45: 70%\n bucket 46: 40%\n bucket 45: 80%\n bucket 46: 50%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n bucket 47: 20%\n Entering block accumulator loop for bucket 48:\n bucket 47: 30%\n bucket 47: 40%\n bucket 48: 10%\n bucket 47: 50%\n bucket 48: 20%\n bucket 48: 30%\n bucket 47: 60%\n bucket 48: 40%\n bucket 47: 70%\n bucket 48: 50%\n bucket 47: 80%\n bucket 48: 60%\n bucket 47: 90%\n bucket 48: 70%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\nGetting block 51 of 60\n Calculating Z arrays for bucket 50\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 51:\n Entering block accumulator loop for bucket 50:\n bucket 51: 10%\n Entering block accumulator loop for bucket 52:\n bucket 50: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 52: 10%\n bucket 50: 20%\n bucket 51: 40%\n bucket 52: 20%\n bucket 51: 50%\n bucket 50: 30%\n bucket 51: 60%\n bucket 52: 30%\n bucket 50: 40%\n bucket 51: 70%\n bucket 52: 40%\n bucket 51: 80%\n bucket 50: 50%\n bucket 51: 90%\n bucket 52: 50%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 50: 60%\n bucket 52: 60%\n bucket 50: 70%\n bucket 52: 70%\n bucket 50: 80%\n bucket 52: 80%\n bucket 50: 90%\n bucket 52: 90%\n bucket 50: 100%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\nGetting block 54 of 60\n bucket 53: 70%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 80%\n bucket 53: 90%\n Entering block accumulator loop for bucket 54:\n bucket 53: 100%\n bucket 54: 10%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\nGetting block 56 of 60\n bucket 55: 60%\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 70%\n bucket 55: 80%\n Entering block accumulator loop for bucket 56:\n bucket 55: 90%\n bucket 55: 100%\n bucket 56: 10%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 10%\n bucket 57: 20%\n Entering block accumulator loop for bucket 58:\n bucket 57: 30%\n bucket 57: 40%\n bucket 58: 10%\n bucket 57: 50%\n bucket 58: 20%\n bucket 58: 30%\n bucket 57: 60%\n bucket 58: 40%\n bucket 57: 70%\n bucket 58: 50%\n bucket 57: 80%\n bucket 58: 60%\n bucket 57: 90%\n bucket 58: 70%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Entering block accumulator loop for bucket 59:\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 10%\n Entering block accumulator loop for bucket 60:\n bucket 59: 20%\n bucket 60: 10%\n bucket 60: 20%\n bucket 59: 30%\n bucket 60: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 60: 40%\n bucket 59: 70%\n bucket 60: 50%\n bucket 59: 80%\n bucket 60: 60%\n bucket 59: 90%\n bucket 60: 70%\n bucket 59: 100%\n bucket 60: 80%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\nGetting block 3 of 60\nGetting block 4 of 60\n bucket 1: 10%\n Reserving size (126) for bucket 3\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 2:\n bucket 1: 20%\n Entering block accumulator loop for bucket 3:\nGetting block 5 of 60\n bucket 2: 10%\n Reserving size (126) for bucket 5\n bucket 3: 10%\n Calculating Z arrays for bucket 5\n bucket 2: 20%\n Entering block accumulator loop for bucket 4:\nGetting block 7 of 60\n Entering block accumulator loop for bucket 5:\n bucket 2: 30%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 4: 10%\n bucket 3: 20%\n Reserving size (126) for bucket 7\n Calculating Z arrays for bucket 6\n bucket 4: 20%\n Calculating Z arrays for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 1: 30%\n bucket 2: 40%\n Entering block accumulator loop for bucket 6:\n bucket 3: 30%\n Calculating Z arrays for bucket 8\n bucket 2: 50%\n bucket 5: 10%\n bucket 4: 30%\n Entering block accumulator loop for bucket 7:\n bucket 2: 60%\n bucket 4: 40%\n bucket 3: 40%\n bucket 6: 10%\n Entering block accumulator loop for bucket 8:\n bucket 4: 50%\n bucket 2: 70%\n bucket 6: 20%\n bucket 3: 50%\n bucket 7: 10%\n bucket 2: 80%\n bucket 4: 60%\n bucket 6: 30%\n bucket 5: 20%\n bucket 4: 70%\n bucket 2: 90%\n bucket 3: 60%\n bucket 1: 40%\n bucket 4: 80%\n bucket 6: 40%\n bucket 7: 20%\n bucket 3: 70%\n bucket 4: 90%\n bucket 8: 10%\n bucket 6: 50%\n bucket 7: 30%\n bucket 2: 100%\n bucket 1: 50%\n Sorting block of length 84 for bucket 2\n bucket 6: 60%\n (Using difference cover)\n bucket 8: 20%\n bucket 7: 40%\n bucket 6: 70%\n bucket 3: 80%\n bucket 1: 60%\n bucket 4: 100%\n bucket 7: 50%\n bucket 3: 90%\n bucket 6: 80%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 5: 30%\n bucket 6: 90%\n bucket 3: 100%\n bucket 7: 60%\n Sorting block of length 106 for bucket 3\n bucket 7: 70%\n (Using difference cover)\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 30%\n bucket 7: 80%\n bucket 5: 40%\n bucket 1: 70%\n bucket 7: 90%\n bucket 8: 40%\n bucket 5: 50%\n bucket 7: 100%\n bucket 1: 80%\n bucket 8: 50%\n bucket 5: 60%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 1: 90%\n bucket 8: 60%\n bucket 5: 70%\n bucket 1: 100%\n bucket 5: 80%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 8: 70%\n bucket 5: 90%\n bucket 8: 80%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\nGetting block 10 of 60\n bucket 9: 10%\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 20%\n bucket 9: 30%\n Entering block accumulator loop for bucket 10:\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 124 for bucket 9\n bucket 10: 70%\n (Using difference cover)\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Entering block accumulator loop for bucket 11:\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 10%\n bucket 11: 20%\n Entering block accumulator loop for bucket 12:\n bucket 11: 30%\n bucket 12: 10%\n bucket 11: 40%\n bucket 12: 20%\n bucket 11: 50%\n bucket 12: 30%\n bucket 11: 60%\n bucket 12: 40%\n bucket 11: 70%\n bucket 12: 50%\n bucket 11: 80%\n bucket 12: 60%\n bucket 11: 90%\n bucket 12: 70%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) 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 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) 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%\nGetting block 15 of 60\n bucket 14: 70%\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 17 of 60\n bucket 14: 80%\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 15:\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 14: 90%\n bucket 15: 10%\n bucket 14: 100%\n Entering block accumulator loop for bucket 17:\n bucket 15: 20%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 30%\n Entering block accumulator loop for bucket 16:\n bucket 15: 40%\n bucket 17: 10%\n bucket 15: 50%\n bucket 16: 10%\n bucket 15: 60%\n bucket 17: 20%\n bucket 15: 70%\n bucket 16: 20%\n bucket 15: 80%\n bucket 17: 30%\n bucket 15: 90%\n bucket 16: 30%\n bucket 17: 40%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 40%\n bucket 17: 50%\n bucket 16: 50%\n bucket 17: 60%\n bucket 16: 60%\n bucket 17: 70%\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n bucket 16: 70%\n bucket 17: 80%\n bucket 16: 80%\n bucket 17: 90%\n bucket 16: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 18:\n Entering block accumulator loop for bucket 19:\n bucket 18: 10%\n bucket 19: 10%\n bucket 18: 20%\n bucket 19: 20%\n bucket 18: 30%\n bucket 19: 30%\n bucket 18: 40%\n bucket 19: 40%\n bucket 19: 50%\n bucket 18: 50%\n bucket 19: 60%\n bucket 18: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 18: 70%\n bucket 19: 90%\n bucket 18: 80%\n bucket 18: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) 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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\nGetting block 22 of 60\n bucket 21: 10%\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 20%\n Entering block accumulator loop for bucket 22:\n bucket 21: 30%\n bucket 22: 10%\n bucket 21: 40%\n bucket 22: 20%\n bucket 21: 50%\n bucket 22: 30%\n bucket 21: 60%\n bucket 21: 70%\n bucket 22: 40%\n bucket 21: 80%\n bucket 22: 50%\n bucket 21: 90%\n bucket 22: 60%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n bucket 22: 70%\n bucket 22: 80%\n (Using difference cover)\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Entering block accumulator loop for bucket 23:\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 24: 10%\n bucket 23: 30%\n bucket 24: 20%\n bucket 23: 40%\n bucket 24: 30%\n bucket 23: 50%\n bucket 24: 40%\n bucket 23: 60%\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) 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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\nGetting block 27 of 60\n Reserving size (126) for bucket 26\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 26\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 26: 10%\n bucket 27: 20%\n bucket 26: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 26: 30%\n bucket 27: 50%\n bucket 26: 40%\n bucket 27: 60%\n bucket 27: 70%\n bucket 26: 50%\n bucket 27: 80%\n bucket 26: 60%\n bucket 27: 90%\n bucket 27: 100%\n bucket 26: 70%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\nGetting block 29 of 60\n bucket 28: 20%\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 30%\n bucket 28: 40%\n Entering block accumulator loop for bucket 29:\n bucket 28: 50%\n bucket 29: 10%\n bucket 28: 60%\n bucket 29: 20%\n bucket 28: 70%\n bucket 29: 30%\n bucket 28: 80%\n bucket 29: 40%\n bucket 28: 90%\n bucket 29: 50%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n Sorting block time: 00:00:00\n bucket 32: 30%\nReturning block of 111 for bucket 31\n bucket 32: 40%\n bucket 32: 50%\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\nGetting block 34 of 60\n bucket 33: 50%\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n Entering block accumulator loop for bucket 34:\n bucket 33: 90%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n bucket 33: 100%\n bucket 34: 10%\n Calculating Z arrays for bucket 35\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 20%\n Entering block accumulator loop for bucket 35:\n bucket 34: 30%\n bucket 35: 10%\n bucket 34: 40%\n bucket 35: 20%\n bucket 34: 50%\n bucket 35: 30%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n Sorting block time: 00:00:00\n bucket 35: 40%\nReturning block of 45 for bucket 33\n bucket 34: 90%\n bucket 35: 50%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n bucket 35: 60%\n (Using difference cover)\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n Entering block accumulator loop for bucket 39:\n bucket 38: 90%\n bucket 38: 100%\n bucket 39: 10%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\nGetting block 42 of 60\n bucket 41: 80%\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 41: 90%\n bucket 41: 100%\n Entering block accumulator loop for bucket 42:\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n bucket 43: 60%\n Entering block accumulator loop for bucket 44:\n bucket 43: 70%\n bucket 44: 10%\n bucket 43: 80%\n bucket 44: 20%\n bucket 43: 90%\n bucket 44: 30%\n bucket 43: 100%\n bucket 44: 40%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Entering block accumulator loop for bucket 45:\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n bucket 45: 20%\n Entering block accumulator loop for bucket 46:\n bucket 45: 30%\n bucket 45: 40%\n bucket 46: 10%\n bucket 45: 50%\n bucket 46: 20%\n bucket 45: 60%\n bucket 46: 30%\n bucket 45: 70%\n bucket 46: 40%\n bucket 45: 80%\n bucket 46: 50%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n bucket 47: 20%\n Entering block accumulator loop for bucket 48:\n bucket 47: 30%\n bucket 47: 40%\n bucket 48: 10%\n bucket 47: 50%\n bucket 48: 20%\n bucket 48: 30%\n bucket 47: 60%\n bucket 48: 40%\n bucket 47: 70%\n bucket 48: 50%\n bucket 47: 80%\n bucket 48: 60%\n bucket 47: 90%\n bucket 48: 70%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\nGetting block 51 of 60\n Calculating Z arrays for bucket 50\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 51:\n Entering block accumulator loop for bucket 50:\n bucket 51: 10%\n Entering block accumulator loop for bucket 52:\n bucket 50: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 52: 10%\n bucket 50: 20%\n bucket 51: 40%\n bucket 52: 20%\n bucket 51: 50%\n bucket 50: 30%\n bucket 51: 60%\n bucket 52: 30%\n bucket 50: 40%\n bucket 51: 70%\n bucket 52: 40%\n bucket 51: 80%\n bucket 50: 50%\n bucket 51: 90%\n bucket 52: 50%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 50: 60%\n bucket 52: 60%\n bucket 50: 70%\n bucket 52: 70%\n bucket 50: 80%\n bucket 52: 80%\n bucket 50: 90%\n bucket 52: 90%\n bucket 50: 100%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\nGetting block 54 of 60\n bucket 53: 70%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 80%\n bucket 53: 90%\n Entering block accumulator loop for bucket 54:\n bucket 53: 100%\n bucket 54: 10%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\nGetting block 56 of 60\n bucket 55: 60%\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 70%\n bucket 55: 80%\n Entering block accumulator loop for bucket 56:\n bucket 55: 90%\n bucket 55: 100%\n bucket 56: 10%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 10%\n bucket 57: 20%\n Entering block accumulator loop for bucket 58:\n bucket 57: 30%\n bucket 57: 40%\n bucket 58: 10%\n bucket 57: 50%\n bucket 58: 20%\n bucket 58: 30%\n bucket 57: 60%\n bucket 58: 40%\n bucket 57: 70%\n bucket 58: 50%\n bucket 57: 80%\n bucket 58: 60%\n bucket 57: 90%\n bucket 58: 70%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Entering block accumulator loop for bucket 59:\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 10%\n Entering block accumulator loop for bucket 60:\n bucket 59: 20%\n bucket 60: 10%\n bucket 60: 20%\n bucket 59: 30%\n bucket 60: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 60: 40%\n bucket 59: 70%\n bucket 60: 50%\n bucket 59: 80%\n bucket 60: 60%\n bucket 59: 90%\n bucket 60: 70%\n bucket 59: 100%\n bucket 60: 80%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:37:18", "plugin": "core", "name": "end_epoch", "raw_value": "1736861838.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:37:18", "plugin": "core", "name": "start_epoch", "raw_value": "1736861838.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 33.09059453010559, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "ab177316c72dfc31"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "2f97fd5d2958797e"}, "library|input_2": {"src": "hda", "id": "9b1b899822d6eb51"}, "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": "baaeb697833af929", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:38:02.196628", "create_time": "2025-01-14T13:37:50.757970", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-9ps88", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/a/b/0/dataset_ab00686c-b476-42de-92b0-950d7023fb2e.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/d/b/5/dataset_db5c8e8c-1ac2-4f51-82db-ea9e50f6b3d3.dat' input_f.fastq.gz && ln -f -s '/galaxy/server/database/objects/8/b/9/dataset_8b9d0ffd-df23-4417-8919-a3c32c46b9dd.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/7/c/d/dataset_7cd06578-7c04-43b5-984d-94d3e126be14.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\": 225, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 226, \"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\": 224, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "ab177316c72dfc31", "src": "hda", "uuid": "ab00686c-b476-42de-92b0-950d7023fb2e"}, "library|input_1": {"id": "2f97fd5d2958797e", "src": "hda", "uuid": "db5c8e8c-1ac2-4f51-82db-ea9e50f6b3d3"}, "library|input_2": {"id": "9b1b899822d6eb51", "src": "hda", "uuid": "8b9d0ffd-df23-4417-8919-a3c32c46b9dd"}}, "outputs": {"output_alignments": {"id": "94213f18fcf46d76", "src": "hda", "uuid": "7cd06578-7c04-43b5-984d-94d3e126be14"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\nGetting block 4 of 60\n bucket 2: 10%\n Entering block accumulator loop for bucket 3:\n bucket 1: 10%\n Reserving size (126) for bucket 4\n bucket 2: 20%\n bucket 1: 20%\n bucket 3: 10%\n bucket 2: 30%\n bucket 1: 30%\n Calculating Z arrays for bucket 4\n bucket 3: 20%\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 2: 40%\n Calculating Z arrays for bucket 5\n bucket 3: 30%\n bucket 1: 40%\n bucket 2: 50%\n Entering block accumulator loop for bucket 4:\n bucket 3: 40%\n bucket 1: 50%\nGetting block 6 of 60\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 1: 60%\n bucket 4: 10%\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 7\n bucket 2: 60%\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 1: 70%\n bucket 2: 70%\n bucket 3: 50%\n bucket 2: 80%\nGetting block 8 of 60\n bucket 4: 20%\n bucket 3: 60%\n bucket 1: 80%\n bucket 5: 10%\n bucket 2: 90%\n bucket 3: 70%\n Entering block accumulator loop for bucket 7:\n Reserving size (126) for bucket 8\n bucket 4: 30%\n bucket 2: 100%\n bucket 1: 90%\n bucket 3: 80%\n Entering block accumulator loop for bucket 6:\n bucket 1: 100%\n bucket 5: 20%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 3: 90%\n Calculating Z arrays for bucket 8\n bucket 5: 30%\n bucket 4: 40%\n bucket 6: 10%\n bucket 3: 100%\n bucket 5: 40%\n bucket 6: 20%\n bucket 7: 10%\n bucket 4: 50%\n Sorting block of length 106 for bucket 3\n bucket 5: 50%\n (Using difference cover)\n Sorting block of length 84 for bucket 2\n bucket 6: 30%\n (Using difference cover)\n bucket 4: 60%\n Entering block accumulator loop for bucket 8:\n bucket 6: 40%\n bucket 5: 60%\n bucket 7: 20%\n bucket 4: 70%\n bucket 5: 70%\n bucket 6: 50%\n bucket 7: 30%\n bucket 5: 80%\n bucket 8: 10%\n bucket 4: 80%\n bucket 5: 90%\n bucket 6: 60%\n bucket 7: 40%\n bucket 8: 20%\n bucket 5: 100%\n bucket 4: 90%\n bucket 6: 70%\n bucket 8: 30%\n bucket 7: 50%\n bucket 4: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 80%\n bucket 7: 60%\n bucket 8: 40%\n Sorting block of length 68 for bucket 4\n bucket 6: 90%\n bucket 7: 70%\n (Using difference cover)\n bucket 8: 50%\n bucket 7: 80%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 60%\n bucket 7: 90%\n bucket 8: 70%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n bucket 8: 80%\n (Using difference cover)\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) 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 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) 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 Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\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 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) 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%\nGetting block 12 of 60\n bucket 11: 40%\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 50%\n bucket 11: 60%\n Entering block accumulator loop for bucket 12:\n bucket 11: 70%\n bucket 12: 10%\n bucket 11: 80%\n bucket 12: 20%\n bucket 11: 90%\n bucket 12: 30%\n bucket 12: 40%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n bucket 12: 50%\n (Using difference cover)\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 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Calculating Z arrays for bucket 13\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 14: 20%\n bucket 13: 30%\n bucket 14: 30%\n bucket 13: 40%\n bucket 14: 40%\n bucket 13: 50%\n bucket 14: 50%\n bucket 13: 60%\n bucket 14: 60%\n bucket 13: 70%\n bucket 14: 70%\n bucket 13: 80%\n bucket 14: 80%\n bucket 13: 90%\n bucket 14: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 15 of 60\n Reserving size (126) 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%\nGetting block 16 of 60\n bucket 15: 90%\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\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 Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) 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 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) 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 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 20:\n Entering block accumulator loop for bucket 19:\n bucket 20: 10%\n bucket 19: 10%\n bucket 20: 20%\n bucket 19: 20%\n bucket 19: 30%\n bucket 20: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 20: 40%\n bucket 19: 70%\n bucket 19: 80%\n bucket 20: 50%\n bucket 19: 90%\n bucket 20: 60%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) 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 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n bucket 22: 10%\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n bucket 22: 20%\n Reserving size (126) for bucket 24\n Entering block accumulator loop for bucket 23:\n Calculating Z arrays for bucket 24\n bucket 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n Entering block accumulator loop for bucket 24:\n bucket 22: 50%\n bucket 23: 20%\n bucket 22: 60%\n bucket 24: 10%\n bucket 23: 30%\n bucket 22: 70%\n bucket 24: 20%\n bucket 23: 40%\n bucket 22: 80%\n bucket 24: 30%\n bucket 23: 50%\n bucket 22: 90%\n bucket 24: 40%\n bucket 23: 60%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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 26: 30%\n bucket 25: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 25: 40%\n bucket 26: 60%\n bucket 25: 50%\n bucket 26: 70%\n bucket 25: 60%\n bucket 26: 80%\n bucket 25: 70%\n bucket 26: 90%\n bucket 25: 80%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 20%\n bucket 27: 30%\n Entering block accumulator loop for bucket 28:\n bucket 27: 40%\n bucket 28: 10%\n bucket 27: 50%\n bucket 28: 20%\n bucket 27: 60%\n bucket 28: 30%\n bucket 27: 70%\n bucket 28: 40%\n bucket 27: 80%\n bucket 28: 50%\n bucket 27: 90%\n bucket 28: 60%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) 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 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\nGetting block 31 of 60\n Calculating Z arrays for bucket 30\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 30: 10%\n bucket 31: 20%\n bucket 30: 20%\n bucket 31: 30%\n bucket 30: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 30: 40%\n bucket 31: 60%\n bucket 30: 50%\n bucket 31: 70%\n bucket 30: 60%\n bucket 31: 80%\n bucket 30: 70%\n bucket 31: 90%\n bucket 30: 80%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\nGetting block 33 of 60\n bucket 32: 40%\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 50%\n bucket 32: 60%\n Entering block accumulator loop for bucket 33:\n bucket 32: 70%\n bucket 32: 80%\n bucket 33: 10%\n bucket 32: 90%\n bucket 33: 20%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n Entering block accumulator loop for bucket 35:\n bucket 34: 10%\n bucket 34: 20%\n bucket 35: 10%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 34: 50%\n bucket 35: 30%\n bucket 34: 60%\n bucket 35: 40%\n bucket 34: 70%\n bucket 35: 50%\n bucket 34: 80%\n bucket 35: 60%\n bucket 34: 90%\n bucket 35: 70%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 38\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 40:\n bucket 38: 10%\n bucket 39: 10%\n bucket 40: 10%\n bucket 38: 20%\n bucket 40: 20%\n bucket 39: 20%\n bucket 40: 30%\n bucket 38: 30%\n bucket 39: 30%\n bucket 40: 40%\n bucket 38: 40%\n bucket 40: 50%\n bucket 39: 40%\n bucket 38: 50%\n bucket 40: 60%\n bucket 39: 50%\n bucket 38: 60%\n bucket 40: 70%\n bucket 39: 60%\n bucket 38: 70%\n bucket 40: 80%\n bucket 39: 70%\n bucket 38: 80%\n bucket 40: 90%\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 38: 90%\n bucket 40: 100%\n bucket 39: 80%\n Sorting block of length 41 for bucket 40\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n (Using difference cover)\n bucket 39: 90%\n Entering block accumulator loop for bucket 41:\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 43:\n Entering block accumulator loop for bucket 42:\n bucket 43: 10%\n bucket 43: 20%\n bucket 42: 10%\n bucket 43: 30%\n bucket 42: 20%\n bucket 43: 40%\n bucket 42: 30%\n bucket 43: 50%\n bucket 42: 40%\n bucket 43: 60%\n bucket 43: 70%\n bucket 42: 50%\n bucket 43: 80%\n bucket 43: 90%\n bucket 42: 60%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\nGetting block 45 of 60\n bucket 44: 50%\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n Entering block accumulator loop for bucket 45:\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n Sorting block time: 00:00:00\n bucket 45: 100%\nReturning block of 67 for bucket 44\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\nGetting block 47 of 60\n Calculating Z arrays for bucket 46\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 46:\n Entering block accumulator loop for bucket 47:\n bucket 46: 10%\n bucket 46: 20%\n bucket 47: 10%\n bucket 46: 30%\n bucket 47: 20%\n bucket 46: 40%\n bucket 47: 30%\n bucket 46: 50%\n bucket 47: 40%\n bucket 46: 60%\n bucket 47: 50%\n bucket 46: 70%\n bucket 46: 80%\n bucket 47: 60%\n bucket 46: 90%\n bucket 47: 70%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 49: 10%\n bucket 48: 20%\n bucket 49: 20%\n bucket 48: 30%\n bucket 49: 30%\n bucket 48: 40%\n bucket 49: 40%\n bucket 48: 50%\n bucket 49: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 49: 60%\n bucket 48: 80%\n bucket 49: 70%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n bucket 49: 80%\n (Using difference cover)\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 10%\n bucket 52: 20%\n Entering block accumulator loop for bucket 53:\n bucket 52: 30%\n bucket 53: 10%\n bucket 52: 40%\n bucket 53: 20%\n bucket 52: 50%\n bucket 53: 30%\n bucket 52: 60%\n bucket 53: 40%\n bucket 52: 70%\n bucket 53: 50%\nGetting block 54 of 60\n bucket 52: 80%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 60%\nGetting block 55 of 60\n Entering block accumulator loop for bucket 54:\n Reserving size (126) for bucket 55\n bucket 52: 90%\n Calculating Z arrays for bucket 55\n bucket 54: 10%\n bucket 53: 70%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 54: 20%\n bucket 53: 80%\n Entering block accumulator loop for bucket 55:\n bucket 53: 90%\n bucket 54: 30%\n bucket 54: 40%\n bucket 55: 10%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n bucket 54: 50%\n bucket 55: 20%\n bucket 54: 60%\n (Using difference cover)\n bucket 54: 70%\n bucket 55: 30%\n bucket 54: 80%\n bucket 55: 40%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 50%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 30%\n bucket 56: 40%\n Entering block accumulator loop for bucket 57:\n bucket 56: 50%\n bucket 57: 10%\n bucket 56: 60%\n bucket 57: 20%\n bucket 56: 70%\n bucket 57: 30%\n bucket 56: 80%\n bucket 57: 40%\n bucket 56: 90%\n bucket 57: 50%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Entering block accumulator loop for bucket 58:\n Calculating Z arrays for bucket 59\n bucket 58: 10%\n Entering block accumulator loop for bucket 59:\n bucket 58: 20%\n bucket 59: 10%\n bucket 58: 30%\n bucket 59: 20%\n bucket 58: 40%\n bucket 59: 30%\n bucket 58: 50%\n bucket 59: 40%\n bucket 58: 60%\n bucket 59: 50%\n bucket 58: 70%\n bucket 59: 60%\n bucket 58: 80%\n bucket 59: 70%\n bucket 58: 90%\n bucket 59: 80%\n bucket 58: 100%\n bucket 59: 90%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\nGetting block 4 of 60\n bucket 2: 10%\n Entering block accumulator loop for bucket 3:\n bucket 1: 10%\n Reserving size (126) for bucket 4\n bucket 2: 20%\n bucket 1: 20%\n bucket 3: 10%\n bucket 2: 30%\n bucket 1: 30%\n Calculating Z arrays for bucket 4\n bucket 3: 20%\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 2: 40%\n Calculating Z arrays for bucket 5\n bucket 3: 30%\n bucket 1: 40%\n bucket 2: 50%\n Entering block accumulator loop for bucket 4:\n bucket 3: 40%\n bucket 1: 50%\nGetting block 6 of 60\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 1: 60%\n bucket 4: 10%\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 7\n bucket 2: 60%\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 1: 70%\n bucket 2: 70%\n bucket 3: 50%\n bucket 2: 80%\nGetting block 8 of 60\n bucket 4: 20%\n bucket 3: 60%\n bucket 1: 80%\n bucket 5: 10%\n bucket 2: 90%\n bucket 3: 70%\n Entering block accumulator loop for bucket 7:\n Reserving size (126) for bucket 8\n bucket 4: 30%\n bucket 2: 100%\n bucket 1: 90%\n bucket 3: 80%\n Entering block accumulator loop for bucket 6:\n bucket 1: 100%\n bucket 5: 20%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 3: 90%\n Calculating Z arrays for bucket 8\n bucket 5: 30%\n bucket 4: 40%\n bucket 6: 10%\n bucket 3: 100%\n bucket 5: 40%\n bucket 6: 20%\n bucket 7: 10%\n bucket 4: 50%\n Sorting block of length 106 for bucket 3\n bucket 5: 50%\n (Using difference cover)\n Sorting block of length 84 for bucket 2\n bucket 6: 30%\n (Using difference cover)\n bucket 4: 60%\n Entering block accumulator loop for bucket 8:\n bucket 6: 40%\n bucket 5: 60%\n bucket 7: 20%\n bucket 4: 70%\n bucket 5: 70%\n bucket 6: 50%\n bucket 7: 30%\n bucket 5: 80%\n bucket 8: 10%\n bucket 4: 80%\n bucket 5: 90%\n bucket 6: 60%\n bucket 7: 40%\n bucket 8: 20%\n bucket 5: 100%\n bucket 4: 90%\n bucket 6: 70%\n bucket 8: 30%\n bucket 7: 50%\n bucket 4: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 80%\n bucket 7: 60%\n bucket 8: 40%\n Sorting block of length 68 for bucket 4\n bucket 6: 90%\n bucket 7: 70%\n (Using difference cover)\n bucket 8: 50%\n bucket 7: 80%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 60%\n bucket 7: 90%\n bucket 8: 70%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n bucket 8: 80%\n (Using difference cover)\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) 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 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) 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 Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\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 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) 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%\nGetting block 12 of 60\n bucket 11: 40%\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 50%\n bucket 11: 60%\n Entering block accumulator loop for bucket 12:\n bucket 11: 70%\n bucket 12: 10%\n bucket 11: 80%\n bucket 12: 20%\n bucket 11: 90%\n bucket 12: 30%\n bucket 12: 40%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n bucket 12: 50%\n (Using difference cover)\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 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Calculating Z arrays for bucket 13\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 14: 20%\n bucket 13: 30%\n bucket 14: 30%\n bucket 13: 40%\n bucket 14: 40%\n bucket 13: 50%\n bucket 14: 50%\n bucket 13: 60%\n bucket 14: 60%\n bucket 13: 70%\n bucket 14: 70%\n bucket 13: 80%\n bucket 14: 80%\n bucket 13: 90%\n bucket 14: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 15 of 60\n Reserving size (126) 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%\nGetting block 16 of 60\n bucket 15: 90%\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\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 Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) 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 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) 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 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 20:\n Entering block accumulator loop for bucket 19:\n bucket 20: 10%\n bucket 19: 10%\n bucket 20: 20%\n bucket 19: 20%\n bucket 19: 30%\n bucket 20: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 20: 40%\n bucket 19: 70%\n bucket 19: 80%\n bucket 20: 50%\n bucket 19: 90%\n bucket 20: 60%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) 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 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n bucket 22: 10%\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n bucket 22: 20%\n Reserving size (126) for bucket 24\n Entering block accumulator loop for bucket 23:\n Calculating Z arrays for bucket 24\n bucket 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n Entering block accumulator loop for bucket 24:\n bucket 22: 50%\n bucket 23: 20%\n bucket 22: 60%\n bucket 24: 10%\n bucket 23: 30%\n bucket 22: 70%\n bucket 24: 20%\n bucket 23: 40%\n bucket 22: 80%\n bucket 24: 30%\n bucket 23: 50%\n bucket 22: 90%\n bucket 24: 40%\n bucket 23: 60%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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 26: 30%\n bucket 25: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 25: 40%\n bucket 26: 60%\n bucket 25: 50%\n bucket 26: 70%\n bucket 25: 60%\n bucket 26: 80%\n bucket 25: 70%\n bucket 26: 90%\n bucket 25: 80%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 20%\n bucket 27: 30%\n Entering block accumulator loop for bucket 28:\n bucket 27: 40%\n bucket 28: 10%\n bucket 27: 50%\n bucket 28: 20%\n bucket 27: 60%\n bucket 28: 30%\n bucket 27: 70%\n bucket 28: 40%\n bucket 27: 80%\n bucket 28: 50%\n bucket 27: 90%\n bucket 28: 60%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) 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 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\nGetting block 31 of 60\n Calculating Z arrays for bucket 30\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 30: 10%\n bucket 31: 20%\n bucket 30: 20%\n bucket 31: 30%\n bucket 30: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 30: 40%\n bucket 31: 60%\n bucket 30: 50%\n bucket 31: 70%\n bucket 30: 60%\n bucket 31: 80%\n bucket 30: 70%\n bucket 31: 90%\n bucket 30: 80%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\nGetting block 33 of 60\n bucket 32: 40%\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 50%\n bucket 32: 60%\n Entering block accumulator loop for bucket 33:\n bucket 32: 70%\n bucket 32: 80%\n bucket 33: 10%\n bucket 32: 90%\n bucket 33: 20%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n Entering block accumulator loop for bucket 35:\n bucket 34: 10%\n bucket 34: 20%\n bucket 35: 10%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 34: 50%\n bucket 35: 30%\n bucket 34: 60%\n bucket 35: 40%\n bucket 34: 70%\n bucket 35: 50%\n bucket 34: 80%\n bucket 35: 60%\n bucket 34: 90%\n bucket 35: 70%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 38\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 40:\n bucket 38: 10%\n bucket 39: 10%\n bucket 40: 10%\n bucket 38: 20%\n bucket 40: 20%\n bucket 39: 20%\n bucket 40: 30%\n bucket 38: 30%\n bucket 39: 30%\n bucket 40: 40%\n bucket 38: 40%\n bucket 40: 50%\n bucket 39: 40%\n bucket 38: 50%\n bucket 40: 60%\n bucket 39: 50%\n bucket 38: 60%\n bucket 40: 70%\n bucket 39: 60%\n bucket 38: 70%\n bucket 40: 80%\n bucket 39: 70%\n bucket 38: 80%\n bucket 40: 90%\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 38: 90%\n bucket 40: 100%\n bucket 39: 80%\n Sorting block of length 41 for bucket 40\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n (Using difference cover)\n bucket 39: 90%\n Entering block accumulator loop for bucket 41:\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 43:\n Entering block accumulator loop for bucket 42:\n bucket 43: 10%\n bucket 43: 20%\n bucket 42: 10%\n bucket 43: 30%\n bucket 42: 20%\n bucket 43: 40%\n bucket 42: 30%\n bucket 43: 50%\n bucket 42: 40%\n bucket 43: 60%\n bucket 43: 70%\n bucket 42: 50%\n bucket 43: 80%\n bucket 43: 90%\n bucket 42: 60%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\nGetting block 45 of 60\n bucket 44: 50%\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n Entering block accumulator loop for bucket 45:\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n Sorting block time: 00:00:00\n bucket 45: 100%\nReturning block of 67 for bucket 44\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\nGetting block 47 of 60\n Calculating Z arrays for bucket 46\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 46:\n Entering block accumulator loop for bucket 47:\n bucket 46: 10%\n bucket 46: 20%\n bucket 47: 10%\n bucket 46: 30%\n bucket 47: 20%\n bucket 46: 40%\n bucket 47: 30%\n bucket 46: 50%\n bucket 47: 40%\n bucket 46: 60%\n bucket 47: 50%\n bucket 46: 70%\n bucket 46: 80%\n bucket 47: 60%\n bucket 46: 90%\n bucket 47: 70%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 49: 10%\n bucket 48: 20%\n bucket 49: 20%\n bucket 48: 30%\n bucket 49: 30%\n bucket 48: 40%\n bucket 49: 40%\n bucket 48: 50%\n bucket 49: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 49: 60%\n bucket 48: 80%\n bucket 49: 70%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n bucket 49: 80%\n (Using difference cover)\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 10%\n bucket 52: 20%\n Entering block accumulator loop for bucket 53:\n bucket 52: 30%\n bucket 53: 10%\n bucket 52: 40%\n bucket 53: 20%\n bucket 52: 50%\n bucket 53: 30%\n bucket 52: 60%\n bucket 53: 40%\n bucket 52: 70%\n bucket 53: 50%\nGetting block 54 of 60\n bucket 52: 80%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 60%\nGetting block 55 of 60\n Entering block accumulator loop for bucket 54:\n Reserving size (126) for bucket 55\n bucket 52: 90%\n Calculating Z arrays for bucket 55\n bucket 54: 10%\n bucket 53: 70%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 54: 20%\n bucket 53: 80%\n Entering block accumulator loop for bucket 55:\n bucket 53: 90%\n bucket 54: 30%\n bucket 54: 40%\n bucket 55: 10%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n bucket 54: 50%\n bucket 55: 20%\n bucket 54: 60%\n (Using difference cover)\n bucket 54: 70%\n bucket 55: 30%\n bucket 54: 80%\n bucket 55: 40%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 50%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 30%\n bucket 56: 40%\n Entering block accumulator loop for bucket 57:\n bucket 56: 50%\n bucket 57: 10%\n bucket 56: 60%\n bucket 57: 20%\n bucket 56: 70%\n bucket 57: 30%\n bucket 56: 80%\n bucket 57: 40%\n bucket 56: 90%\n bucket 57: 50%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Entering block accumulator loop for bucket 58:\n Calculating Z arrays for bucket 59\n bucket 58: 10%\n Entering block accumulator loop for bucket 59:\n bucket 58: 20%\n bucket 59: 10%\n bucket 58: 30%\n bucket 59: 20%\n bucket 58: 40%\n bucket 59: 30%\n bucket 58: 50%\n bucket 59: 40%\n bucket 58: 60%\n bucket 59: 50%\n bucket 58: 70%\n bucket 59: 60%\n bucket 58: 80%\n bucket 59: 70%\n bucket 58: 90%\n bucket 59: 80%\n bucket 58: 100%\n bucket 59: 90%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:37:53", "plugin": "core", "name": "end_epoch", "raw_value": "1736861873.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:37:52", "plugin": "core", "name": "start_epoch", "raw_value": "1736861872.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 33.92531609535217, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "2faad319b061412d"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "78773509467966f4"}, "library|input_2": {"src": "hda", "id": "8d94870dfa7b4064"}, "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": "809c769c23542a1b", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:38:36.081826", "create_time": "2025-01-14T13:38:23.566157", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-smzql", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/f/b/c/dataset_fbc6fb3f-b4e8-4582-89f6-2ec11c949474.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/6/1/f/dataset_61f16d8f-c47a-4989-8068-1bf81db1a826.dat' input_f.fastq.bz2 && ln -f -s '/galaxy/server/database/objects/8/0/b/dataset_80b7f3d7-baa3-4da3-b3bf-0bb1ea4c9016.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/3/4/0/dataset_340bdf0d-231c-4d56-963e-07ee5cc4869f.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\": 229, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 230, \"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\": 228, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "2faad319b061412d", "src": "hda", "uuid": "fbc6fb3f-b4e8-4582-89f6-2ec11c949474"}, "library|input_1": {"id": "78773509467966f4", "src": "hda", "uuid": "61f16d8f-c47a-4989-8068-1bf81db1a826"}, "library|input_2": {"id": "8d94870dfa7b4064", "src": "hda", "uuid": "80b7f3d7-baa3-4da3-b3bf-0bb1ea4c9016"}}, "outputs": {"output_alignments": {"id": "f91b7bdcaee190db", "src": "hda", "uuid": "340bdf0d-231c-4d56-963e-07ee5cc4869f"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 1\nGetting block 3 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 3\nGetting block 5 of 60\nGetting block 6 of 60\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n Reserving size (126) for bucket 5\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\nGetting block 8 of 60\n Entering block accumulator loop for bucket 4:\n bucket 3: 10%\n Calculating Z arrays for bucket 5\nGetting block 7 of 60\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 7\n bucket 1: 10%\n bucket 5: 10%\n Entering block accumulator loop for bucket 6:\n bucket 4: 10%\n bucket 5: 20%\n bucket 3: 20%\n Entering block accumulator loop for bucket 2:\n bucket 4: 20%\n Calculating Z arrays for bucket 7\n bucket 3: 30%\n bucket 1: 20%\n bucket 4: 30%\n bucket 2: 10%\n bucket 5: 30%\n bucket 6: 10%\n Entering block accumulator loop for bucket 7:\n bucket 5: 40%\n bucket 2: 20%\n Reserving size (126) for bucket 8\n bucket 5: 50%\n bucket 2: 30%\n Calculating Z arrays for bucket 8\n bucket 5: 60%\n bucket 7: 10%\n bucket 1: 30%\n bucket 2: 40%\n bucket 3: 40%\n bucket 7: 20%\n bucket 2: 50%\n bucket 1: 40%\n bucket 4: 40%\n bucket 5: 70%\n bucket 2: 60%\n bucket 3: 50%\n Entering block accumulator loop for bucket 8:\n bucket 6: 20%\n bucket 2: 70%\n bucket 1: 50%\n bucket 6: 30%\n bucket 5: 80%\n bucket 8: 10%\n bucket 3: 60%\n bucket 1: 60%\n bucket 6: 40%\n bucket 4: 50%\n bucket 3: 70%\n bucket 6: 50%\n bucket 4: 60%\n bucket 5: 90%\n bucket 8: 20%\n bucket 2: 80%\n bucket 5: 100%\n bucket 6: 60%\n bucket 2: 90%\n bucket 1: 70%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 30%\n bucket 8: 30%\n bucket 4: 70%\n bucket 6: 70%\n bucket 3: 80%\n bucket 1: 80%\n bucket 7: 40%\n bucket 3: 90%\n bucket 8: 40%\n bucket 2: 100%\n bucket 4: 80%\n bucket 7: 50%\n bucket 1: 90%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 8: 50%\n bucket 3: 100%\n bucket 1: 100%\n bucket 8: 60%\n bucket 4: 90%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Sorting block of length 42 for bucket 1\n bucket 6: 80%\n (Using difference cover)\n bucket 4: 100%\n bucket 7: 60%\n bucket 6: 90%\n bucket 8: 70%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 7: 70%\n bucket 8: 80%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 7: 80%\n bucket 8: 90%\n bucket 7: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) 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%\nGetting block 10 of 60\n bucket 9: 30%\nGetting block 11 of 60\n bucket 9: 40%\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n Entering block accumulator loop for bucket 11:\n bucket 9: 90%\n Entering block accumulator loop for bucket 10:\n bucket 11: 10%\n bucket 10: 10%\n bucket 9: 100%\n bucket 11: 20%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 20%\n bucket 10: 30%\n bucket 11: 30%\n bucket 10: 40%\n bucket 11: 40%\n bucket 10: 50%\n bucket 11: 50%\n bucket 10: 60%\n bucket 11: 60%\n bucket 10: 70%\n bucket 11: 70%\n bucket 10: 80%\n bucket 11: 80%\n bucket 10: 90%\n bucket 11: 90%\n bucket 10: 100%\n bucket 11: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 13:\n bucket 12: 10%\n bucket 12: 20%\n bucket 13: 10%\n bucket 12: 30%\n bucket 13: 20%\n bucket 12: 40%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\n bucket 13: 40%\n bucket 12: 70%\n bucket 13: 50%\n bucket 12: 80%\n bucket 13: 60%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\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 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 10%\n bucket 14: 20%\n Entering block accumulator loop for bucket 15:\n bucket 14: 30%\n bucket 15: 10%\n bucket 14: 40%\n bucket 15: 20%\n bucket 15: 30%\n bucket 14: 50%\n bucket 15: 40%\n bucket 14: 60%\n bucket 15: 50%\n bucket 14: 70%\n bucket 15: 60%\n bucket 14: 80%\n bucket 15: 70%\n bucket 14: 90%\n bucket 15: 80%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n Entering block accumulator loop for bucket 17:\n bucket 16: 20%\n bucket 17: 10%\n bucket 16: 30%\n bucket 17: 20%\n bucket 16: 40%\n bucket 17: 30%\n bucket 16: 50%\n bucket 17: 40%\n bucket 16: 60%\n bucket 17: 50%\n bucket 16: 70%\n bucket 17: 60%\n bucket 16: 80%\n bucket 17: 70%\n bucket 16: 90%\n bucket 17: 80%\n bucket 16: 100%\n bucket 17: 90%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Entering block accumulator loop for bucket 18:\n Calculating Z arrays for bucket 19\n bucket 18: 10%\n bucket 18: 20%\n Entering block accumulator loop for bucket 19:\n bucket 18: 30%\n bucket 19: 10%\n bucket 19: 20%\n bucket 18: 40%\n bucket 19: 30%\n bucket 18: 50%\n bucket 19: 40%\n bucket 18: 60%\n bucket 19: 50%\n bucket 18: 70%\n bucket 19: 60%\n bucket 18: 80%\n bucket 19: 70%\n bucket 18: 90%\n bucket 19: 80%\n bucket 18: 100%\n bucket 19: 90%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\nGetting block 21 of 60\n bucket 20: 10%\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 20%\n bucket 20: 30%\n Entering block accumulator loop for bucket 21:\n bucket 20: 40%\n bucket 21: 10%\n bucket 20: 50%\n bucket 21: 20%\n bucket 20: 60%\n bucket 21: 30%\n bucket 20: 70%\n bucket 21: 40%\n bucket 20: 80%\n bucket 21: 50%\n bucket 20: 90%\n bucket 21: 60%\n bucket 20: 100%\n bucket 21: 70%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\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 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 Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) 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 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 25\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 25:\n bucket 26: 10%\n bucket 25: 10%\n bucket 26: 20%\n bucket 25: 20%\n bucket 26: 30%\n bucket 25: 30%\n bucket 26: 40%\n bucket 25: 40%\n bucket 26: 50%\n bucket 25: 50%\n bucket 26: 60%\n bucket 25: 60%\n bucket 26: 70%\n bucket 25: 70%\n bucket 26: 80%\n bucket 25: 80%\n bucket 25: 90%\n bucket 26: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\nGetting block 27 of 60\n Sorting block time: 00:00:00\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\nReturning block of 108 for bucket 26\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 67 for bucket 25\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 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) 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%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\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 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 80%\n Calculating Z arrays for bucket 31\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 32:\n Entering block accumulator loop for bucket 33:\n bucket 32: 10%\n bucket 33: 10%\n bucket 32: 20%\n bucket 33: 20%\n bucket 32: 30%\n bucket 33: 30%\n bucket 32: 40%\n bucket 33: 40%\n bucket 32: 50%\n bucket 33: 50%\n bucket 32: 60%\n bucket 33: 60%\n bucket 32: 70%\n bucket 33: 70%\n bucket 32: 80%\n bucket 33: 80%\n bucket 32: 90%\n bucket 33: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 50%\n Entering block accumulator loop for bucket 35:\n bucket 34: 60%\n bucket 35: 10%\n bucket 34: 70%\n bucket 35: 20%\n bucket 34: 80%\n bucket 35: 30%\n bucket 35: 40%\n bucket 34: 90%\n bucket 35: 50%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\nGetting block 37 of 60\n bucket 36: 10%\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 20%\n bucket 36: 30%\n Entering block accumulator loop for bucket 37:\n bucket 36: 40%\n bucket 37: 10%\n bucket 36: 50%\n bucket 36: 60%\n bucket 37: 20%\n bucket 36: 70%\n bucket 37: 30%\n bucket 36: 80%\n bucket 37: 40%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Entering block accumulator loop for bucket 38:\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n Entering block accumulator loop for bucket 39:\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 39: 20%\n bucket 38: 40%\n bucket 39: 30%\n bucket 38: 50%\n bucket 39: 40%\n bucket 39: 50%\n bucket 38: 60%\n bucket 39: 60%\n bucket 38: 70%\n bucket 39: 70%\n bucket 38: 80%\n bucket 39: 80%\n bucket 38: 90%\n bucket 39: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\n bucket 41: 20%\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 41: 50%\n bucket 40: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n bucket 41: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n bucket 43: 50%\n Calculating Z arrays for bucket 44\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n Entering block accumulator loop for bucket 44:\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 50%\n Entering block accumulator loop for bucket 46:\n bucket 45: 60%\n bucket 46: 10%\n bucket 45: 70%\n bucket 46: 20%\n bucket 45: 80%\n bucket 46: 30%\n bucket 45: 90%\n bucket 46: 40%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 48:\n bucket 49: 10%\n bucket 49: 20%\n bucket 48: 10%\n bucket 49: 30%\n bucket 48: 20%\n bucket 49: 40%\n bucket 48: 30%\n bucket 49: 50%\n bucket 48: 40%\n bucket 49: 60%\n bucket 48: 50%\n bucket 49: 70%\n bucket 48: 60%\n bucket 49: 80%\n bucket 48: 70%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 30%\n bucket 50: 40%\n Entering block accumulator loop for bucket 51:\n bucket 50: 50%\n bucket 51: 10%\n bucket 50: 60%\n bucket 51: 20%\n bucket 50: 70%\n bucket 51: 30%\n bucket 50: 80%\n bucket 51: 40%\n bucket 50: 90%\n bucket 51: 50%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Entering block accumulator loop for bucket 53:\n Calculating Z arrays for bucket 54\n bucket 53: 10%\n bucket 53: 20%\n Entering block accumulator loop for bucket 54:\n bucket 53: 30%\n bucket 53: 40%\n bucket 54: 10%\n bucket 53: 50%\n bucket 54: 20%\n bucket 53: 60%\n bucket 54: 30%\n bucket 53: 70%\n bucket 54: 40%\n bucket 53: 80%\n bucket 54: 50%\n bucket 53: 90%\n bucket 54: 60%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n bucket 58: 10%\n Calculating Z arrays for bucket 59\n bucket 58: 20%\n Entering block accumulator loop for bucket 59:\n bucket 58: 30%\n bucket 59: 10%\n bucket 58: 40%\n bucket 59: 20%\n bucket 58: 50%\n bucket 59: 30%\n bucket 58: 60%\n bucket 59: 40%\n bucket 58: 70%\n bucket 59: 50%\n bucket 58: 80%\n bucket 59: 60%\n bucket 58: 90%\n bucket 59: 70%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n bucket 59: 80%\n (Using difference cover)\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 1\nGetting block 3 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 3\nGetting block 5 of 60\nGetting block 6 of 60\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n Reserving size (126) for bucket 5\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\nGetting block 8 of 60\n Entering block accumulator loop for bucket 4:\n bucket 3: 10%\n Calculating Z arrays for bucket 5\nGetting block 7 of 60\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 7\n bucket 1: 10%\n bucket 5: 10%\n Entering block accumulator loop for bucket 6:\n bucket 4: 10%\n bucket 5: 20%\n bucket 3: 20%\n Entering block accumulator loop for bucket 2:\n bucket 4: 20%\n Calculating Z arrays for bucket 7\n bucket 3: 30%\n bucket 1: 20%\n bucket 4: 30%\n bucket 2: 10%\n bucket 5: 30%\n bucket 6: 10%\n Entering block accumulator loop for bucket 7:\n bucket 5: 40%\n bucket 2: 20%\n Reserving size (126) for bucket 8\n bucket 5: 50%\n bucket 2: 30%\n Calculating Z arrays for bucket 8\n bucket 5: 60%\n bucket 7: 10%\n bucket 1: 30%\n bucket 2: 40%\n bucket 3: 40%\n bucket 7: 20%\n bucket 2: 50%\n bucket 1: 40%\n bucket 4: 40%\n bucket 5: 70%\n bucket 2: 60%\n bucket 3: 50%\n Entering block accumulator loop for bucket 8:\n bucket 6: 20%\n bucket 2: 70%\n bucket 1: 50%\n bucket 6: 30%\n bucket 5: 80%\n bucket 8: 10%\n bucket 3: 60%\n bucket 1: 60%\n bucket 6: 40%\n bucket 4: 50%\n bucket 3: 70%\n bucket 6: 50%\n bucket 4: 60%\n bucket 5: 90%\n bucket 8: 20%\n bucket 2: 80%\n bucket 5: 100%\n bucket 6: 60%\n bucket 2: 90%\n bucket 1: 70%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 30%\n bucket 8: 30%\n bucket 4: 70%\n bucket 6: 70%\n bucket 3: 80%\n bucket 1: 80%\n bucket 7: 40%\n bucket 3: 90%\n bucket 8: 40%\n bucket 2: 100%\n bucket 4: 80%\n bucket 7: 50%\n bucket 1: 90%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 8: 50%\n bucket 3: 100%\n bucket 1: 100%\n bucket 8: 60%\n bucket 4: 90%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Sorting block of length 42 for bucket 1\n bucket 6: 80%\n (Using difference cover)\n bucket 4: 100%\n bucket 7: 60%\n bucket 6: 90%\n bucket 8: 70%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 7: 70%\n bucket 8: 80%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 7: 80%\n bucket 8: 90%\n bucket 7: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) 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%\nGetting block 10 of 60\n bucket 9: 30%\nGetting block 11 of 60\n bucket 9: 40%\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n Entering block accumulator loop for bucket 11:\n bucket 9: 90%\n Entering block accumulator loop for bucket 10:\n bucket 11: 10%\n bucket 10: 10%\n bucket 9: 100%\n bucket 11: 20%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 20%\n bucket 10: 30%\n bucket 11: 30%\n bucket 10: 40%\n bucket 11: 40%\n bucket 10: 50%\n bucket 11: 50%\n bucket 10: 60%\n bucket 11: 60%\n bucket 10: 70%\n bucket 11: 70%\n bucket 10: 80%\n bucket 11: 80%\n bucket 10: 90%\n bucket 11: 90%\n bucket 10: 100%\n bucket 11: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 13:\n bucket 12: 10%\n bucket 12: 20%\n bucket 13: 10%\n bucket 12: 30%\n bucket 13: 20%\n bucket 12: 40%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\n bucket 13: 40%\n bucket 12: 70%\n bucket 13: 50%\n bucket 12: 80%\n bucket 13: 60%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\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 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 10%\n bucket 14: 20%\n Entering block accumulator loop for bucket 15:\n bucket 14: 30%\n bucket 15: 10%\n bucket 14: 40%\n bucket 15: 20%\n bucket 15: 30%\n bucket 14: 50%\n bucket 15: 40%\n bucket 14: 60%\n bucket 15: 50%\n bucket 14: 70%\n bucket 15: 60%\n bucket 14: 80%\n bucket 15: 70%\n bucket 14: 90%\n bucket 15: 80%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n Entering block accumulator loop for bucket 17:\n bucket 16: 20%\n bucket 17: 10%\n bucket 16: 30%\n bucket 17: 20%\n bucket 16: 40%\n bucket 17: 30%\n bucket 16: 50%\n bucket 17: 40%\n bucket 16: 60%\n bucket 17: 50%\n bucket 16: 70%\n bucket 17: 60%\n bucket 16: 80%\n bucket 17: 70%\n bucket 16: 90%\n bucket 17: 80%\n bucket 16: 100%\n bucket 17: 90%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Entering block accumulator loop for bucket 18:\n Calculating Z arrays for bucket 19\n bucket 18: 10%\n bucket 18: 20%\n Entering block accumulator loop for bucket 19:\n bucket 18: 30%\n bucket 19: 10%\n bucket 19: 20%\n bucket 18: 40%\n bucket 19: 30%\n bucket 18: 50%\n bucket 19: 40%\n bucket 18: 60%\n bucket 19: 50%\n bucket 18: 70%\n bucket 19: 60%\n bucket 18: 80%\n bucket 19: 70%\n bucket 18: 90%\n bucket 19: 80%\n bucket 18: 100%\n bucket 19: 90%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\nGetting block 21 of 60\n bucket 20: 10%\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 20%\n bucket 20: 30%\n Entering block accumulator loop for bucket 21:\n bucket 20: 40%\n bucket 21: 10%\n bucket 20: 50%\n bucket 21: 20%\n bucket 20: 60%\n bucket 21: 30%\n bucket 20: 70%\n bucket 21: 40%\n bucket 20: 80%\n bucket 21: 50%\n bucket 20: 90%\n bucket 21: 60%\n bucket 20: 100%\n bucket 21: 70%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\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 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 Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) 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 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 25\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 25:\n bucket 26: 10%\n bucket 25: 10%\n bucket 26: 20%\n bucket 25: 20%\n bucket 26: 30%\n bucket 25: 30%\n bucket 26: 40%\n bucket 25: 40%\n bucket 26: 50%\n bucket 25: 50%\n bucket 26: 60%\n bucket 25: 60%\n bucket 26: 70%\n bucket 25: 70%\n bucket 26: 80%\n bucket 25: 80%\n bucket 25: 90%\n bucket 26: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\nGetting block 27 of 60\n Sorting block time: 00:00:00\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\nReturning block of 108 for bucket 26\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 67 for bucket 25\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 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) 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%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\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 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 80%\n Calculating Z arrays for bucket 31\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 32:\n Entering block accumulator loop for bucket 33:\n bucket 32: 10%\n bucket 33: 10%\n bucket 32: 20%\n bucket 33: 20%\n bucket 32: 30%\n bucket 33: 30%\n bucket 32: 40%\n bucket 33: 40%\n bucket 32: 50%\n bucket 33: 50%\n bucket 32: 60%\n bucket 33: 60%\n bucket 32: 70%\n bucket 33: 70%\n bucket 32: 80%\n bucket 33: 80%\n bucket 32: 90%\n bucket 33: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 50%\n Entering block accumulator loop for bucket 35:\n bucket 34: 60%\n bucket 35: 10%\n bucket 34: 70%\n bucket 35: 20%\n bucket 34: 80%\n bucket 35: 30%\n bucket 35: 40%\n bucket 34: 90%\n bucket 35: 50%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\nGetting block 37 of 60\n bucket 36: 10%\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 20%\n bucket 36: 30%\n Entering block accumulator loop for bucket 37:\n bucket 36: 40%\n bucket 37: 10%\n bucket 36: 50%\n bucket 36: 60%\n bucket 37: 20%\n bucket 36: 70%\n bucket 37: 30%\n bucket 36: 80%\n bucket 37: 40%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Entering block accumulator loop for bucket 38:\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n Entering block accumulator loop for bucket 39:\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 39: 20%\n bucket 38: 40%\n bucket 39: 30%\n bucket 38: 50%\n bucket 39: 40%\n bucket 39: 50%\n bucket 38: 60%\n bucket 39: 60%\n bucket 38: 70%\n bucket 39: 70%\n bucket 38: 80%\n bucket 39: 80%\n bucket 38: 90%\n bucket 39: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\n bucket 41: 20%\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 41: 50%\n bucket 40: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n bucket 41: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n bucket 43: 50%\n Calculating Z arrays for bucket 44\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n Entering block accumulator loop for bucket 44:\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 50%\n Entering block accumulator loop for bucket 46:\n bucket 45: 60%\n bucket 46: 10%\n bucket 45: 70%\n bucket 46: 20%\n bucket 45: 80%\n bucket 46: 30%\n bucket 45: 90%\n bucket 46: 40%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 48:\n bucket 49: 10%\n bucket 49: 20%\n bucket 48: 10%\n bucket 49: 30%\n bucket 48: 20%\n bucket 49: 40%\n bucket 48: 30%\n bucket 49: 50%\n bucket 48: 40%\n bucket 49: 60%\n bucket 48: 50%\n bucket 49: 70%\n bucket 48: 60%\n bucket 49: 80%\n bucket 48: 70%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 30%\n bucket 50: 40%\n Entering block accumulator loop for bucket 51:\n bucket 50: 50%\n bucket 51: 10%\n bucket 50: 60%\n bucket 51: 20%\n bucket 50: 70%\n bucket 51: 30%\n bucket 50: 80%\n bucket 51: 40%\n bucket 50: 90%\n bucket 51: 50%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Entering block accumulator loop for bucket 53:\n Calculating Z arrays for bucket 54\n bucket 53: 10%\n bucket 53: 20%\n Entering block accumulator loop for bucket 54:\n bucket 53: 30%\n bucket 53: 40%\n bucket 54: 10%\n bucket 53: 50%\n bucket 54: 20%\n bucket 53: 60%\n bucket 54: 30%\n bucket 53: 70%\n bucket 54: 40%\n bucket 53: 80%\n bucket 54: 50%\n bucket 53: 90%\n bucket 54: 60%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n bucket 58: 10%\n Calculating Z arrays for bucket 59\n bucket 58: 20%\n Entering block accumulator loop for bucket 59:\n bucket 58: 30%\n bucket 59: 10%\n bucket 58: 40%\n bucket 59: 20%\n bucket 58: 50%\n bucket 59: 30%\n bucket 58: 60%\n bucket 59: 40%\n bucket 58: 70%\n bucket 59: 50%\n bucket 58: 80%\n bucket 59: 60%\n bucket 58: 90%\n bucket 59: 70%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n bucket 59: 80%\n (Using difference cover)\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:38:25", "plugin": "core", "name": "end_epoch", "raw_value": "1736861905.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:38:24", "plugin": "core", "name": "start_epoch", "raw_value": "1736861904.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "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": 32.568490982055664, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "62ec54d8a6811c68"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "14bae08b3b2764fc"}, "library|input_2": {"src": "hda", "id": "1819b722386e55aa"}, "library|rna_strandness": "FR", "library|type": "paired"}, "job": {"model_class": "Job", "id": "c6c8d129e99d243b", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:39:09.109616", "create_time": "2025-01-14T13:38:57.686396", "galaxy_version": "23.1", "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}", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-nljq2", "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/5/4/8/dataset_5486bafd-2882-4932-9669-d1b6e6077adb.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/6/a/1/dataset_6a154439-ad45-45f3-b3ae-4e6bccd0c441.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/e/2/0/dataset_e2081b37-21ae-4eb0-94ed-28cde586dcb7.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/2/a/e/dataset_2aed28db-ed2c-48bb-b12e-cb574b8ea64a.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\": 233, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 234, \"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\": 232, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "62ec54d8a6811c68", "src": "hda", "uuid": "5486bafd-2882-4932-9669-d1b6e6077adb"}, "library|input_1": {"id": "14bae08b3b2764fc", "src": "hda", "uuid": "6a154439-ad45-45f3-b3ae-4e6bccd0c441"}, "library|input_2": {"id": "1819b722386e55aa", "src": "hda", "uuid": "e2081b37-21ae-4eb0-94ed-28cde586dcb7"}}, "outputs": {"output_alignments": {"id": "d2087a8a16014901", "src": "hda", "uuid": "2aed28db-ed2c-48bb-b12e-cb574b8ea64a"}}, "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 3 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n Reserving size (126) for bucket 3\nGetting block 4 of 60\n Calculating Z arrays for bucket 3\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 5\n Reserving size (126) for bucket 4\nGetting block 6 of 60\n Entering block accumulator loop for bucket 2:\n bucket 1: 10%\n Reserving size (126) for bucket 6\nGetting block 7 of 60\n Reserving size (126) for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 5:\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 4\n bucket 2: 10%\n Calculating Z arrays for bucket 8\n bucket 1: 20%\n bucket 3: 10%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 7:\n bucket 5: 10%\n Entering block accumulator loop for bucket 8:\n bucket 6: 10%\n bucket 1: 30%\n bucket 7: 10%\n bucket 4: 10%\n bucket 1: 40%\n bucket 6: 20%\n bucket 5: 20%\n bucket 8: 10%\n bucket 4: 20%\n bucket 6: 30%\n bucket 2: 20%\n bucket 7: 20%\n bucket 3: 20%\n bucket 6: 40%\n bucket 8: 20%\n bucket 3: 30%\n bucket 4: 30%\n bucket 6: 50%\n bucket 2: 30%\n bucket 3: 40%\n bucket 1: 50%\n bucket 4: 40%\n bucket 8: 30%\n bucket 6: 60%\n bucket 2: 40%\n bucket 4: 50%\n bucket 5: 30%\n bucket 7: 30%\n bucket 8: 40%\n bucket 1: 60%\n bucket 5: 40%\n bucket 6: 70%\n bucket 3: 50%\n bucket 4: 60%\n bucket 6: 80%\n bucket 8: 50%\n bucket 1: 70%\n bucket 3: 60%\n bucket 6: 90%\n bucket 2: 50%\n bucket 3: 70%\n bucket 1: 80%\n bucket 5: 50%\n bucket 6: 100%\n bucket 7: 40%\n bucket 3: 80%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 4: 70%\n bucket 2: 60%\n bucket 3: 90%\n bucket 1: 90%\n bucket 4: 80%\n bucket 7: 50%\n bucket 5: 60%\n bucket 8: 60%\n bucket 2: 70%\n bucket 7: 60%\n bucket 5: 70%\n bucket 8: 70%\n bucket 4: 90%\n bucket 3: 100%\n bucket 7: 70%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 2: 80%\n bucket 5: 80%\n bucket 4: 100%\n bucket 8: 80%\n bucket 5: 90%\n Sorting block of length 68 for bucket 4\n bucket 2: 90%\n bucket 1: 100%\n bucket 5: 100%\n (Using difference cover)\n bucket 8: 90%\n bucket 2: 100%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Sorting block of length 63 for bucket 5\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n (Using difference cover)\n bucket 8: 100%\n Sorting block time: 00:00:00\n Sorting block of length 94 for bucket 8\n (Using difference cover)\nReturning block of 91 for bucket 6\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\nGetting block 10 of 60\n bucket 9: 10%\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n Entering block accumulator loop for bucket 10:\n bucket 9: 50%\n bucket 10: 10%\n bucket 9: 60%\n bucket 10: 20%\n bucket 9: 70%\n bucket 10: 30%\n bucket 9: 80%\n bucket 10: 40%\n bucket 9: 90%\n bucket 10: 50%\n bucket 10: 60%\n bucket 9: 100%\n Sorting block of length 124 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 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Reserving size (126) 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%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n bucket 12: 20%\n Calculating Z arrays for bucket 13\n bucket 11: 20%\n bucket 12: 30%\n Entering block accumulator loop for bucket 13:\n bucket 11: 30%\n bucket 12: 40%\n bucket 11: 40%\n bucket 13: 10%\n bucket 12: 50%\n bucket 11: 50%\n bucket 13: 20%\n bucket 12: 60%\n bucket 11: 60%\n bucket 13: 30%\n bucket 12: 70%\n bucket 11: 70%\n bucket 12: 80%\n bucket 13: 40%\n bucket 12: 90%\n bucket 13: 50%\n bucket 11: 80%\n bucket 13: 60%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 70%\n bucket 11: 90%\n bucket 13: 80%\n bucket 13: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 14 of 60\n Reserving size (126) 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%\nGetting block 15 of 60\n bucket 14: 70%\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 80%\n bucket 14: 90%\n Entering block accumulator loop for bucket 15:\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\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 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 60\n Reserving size (126) 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 17: 30%\n bucket 16: 60%\n bucket 17: 40%\n bucket 16: 70%\n bucket 17: 50%\n bucket 16: 80%\n bucket 17: 60%\n bucket 16: 90%\n bucket 17: 70%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) 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%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\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 122 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 bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Reserving size (126) for bucket 20\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 20: 30%\n bucket 21: 50%\n bucket 20: 40%\n bucket 21: 60%\n bucket 21: 70%\n bucket 20: 50%\n bucket 21: 80%\n bucket 20: 60%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) 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 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 80 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\n Reserving size (126) 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%\nGetting block 25 of 60\n bucket 24: 60%\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 70%\n bucket 24: 80%\n Entering block accumulator loop for bucket 25:\n bucket 24: 90%\n bucket 25: 10%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n bucket 25: 20%\n (Using difference cover)\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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) 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 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Entering block accumulator loop for bucket 28:\n Calculating Z arrays for bucket 29\n bucket 28: 10%\n Entering block accumulator loop for bucket 29:\n bucket 28: 20%\n bucket 28: 30%\n bucket 29: 10%\n bucket 28: 40%\n bucket 29: 20%\n bucket 28: 50%\n bucket 29: 30%\n bucket 28: 60%\n bucket 29: 40%\n bucket 28: 70%\n bucket 29: 50%\n bucket 28: 80%\n bucket 29: 60%\n bucket 28: 90%\n bucket 29: 70%\n bucket 28: 100%\n bucket 29: 80%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n Entering block accumulator loop for bucket 31:\n bucket 30: 20%\n bucket 31: 10%\n bucket 30: 30%\n bucket 31: 20%\n bucket 30: 40%\n bucket 31: 30%\n bucket 30: 50%\n bucket 31: 40%\n bucket 30: 60%\n bucket 31: 50%\n bucket 30: 70%\n bucket 31: 60%\n bucket 30: 80%\n bucket 31: 70%\n bucket 30: 90%\n bucket 31: 80%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\n bucket 32: 40%\n bucket 32: 50%\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\nGetting block 35 of 60\n bucket 34: 60%\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 70%\n bucket 34: 80%\n Entering block accumulator loop for bucket 35:\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\nGetting block 37 of 60\n bucket 36: 40%\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 50%\n Entering block accumulator loop for bucket 37:\n bucket 36: 60%\n bucket 37: 10%\n bucket 36: 70%\n bucket 37: 20%\n bucket 36: 80%\n bucket 37: 30%\n bucket 36: 90%\n bucket 37: 40%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n bucket 38: 20%\n Entering block accumulator loop for bucket 39:\n bucket 38: 30%\n bucket 39: 10%\n bucket 38: 40%\n bucket 39: 20%\n bucket 38: 50%\n bucket 39: 30%\n bucket 39: 40%\n bucket 38: 60%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 38: 70%\n bucket 39: 80%\n bucket 38: 80%\n bucket 39: 90%\n bucket 38: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 40:\n bucket 41: 10%\n bucket 40: 10%\n bucket 41: 20%\n bucket 40: 20%\n bucket 41: 30%\n bucket 40: 30%\n bucket 41: 40%\n bucket 40: 40%\n bucket 41: 50%\n bucket 40: 50%\n bucket 41: 60%\n bucket 40: 60%\n bucket 41: 70%\n bucket 40: 70%\n bucket 41: 80%\n bucket 40: 80%\n bucket 41: 90%\n bucket 40: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n bucket 42: 60%\n Calculating Z arrays for bucket 43\n bucket 42: 70%\n bucket 42: 80%\n Entering block accumulator loop for bucket 43:\n bucket 42: 90%\n bucket 42: 100%\n bucket 43: 10%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n Entering block accumulator loop for bucket 45:\n bucket 44: 20%\n bucket 45: 10%\n bucket 44: 30%\n bucket 44: 40%\n bucket 45: 20%\n bucket 44: 50%\n bucket 45: 30%\n bucket 44: 60%\n bucket 44: 70%\n bucket 45: 40%\n bucket 44: 80%\n bucket 45: 50%\n bucket 44: 90%\n bucket 45: 60%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 47:\n Entering block accumulator loop for bucket 48:\n bucket 47: 10%\n bucket 48: 10%\n bucket 48: 20%\n bucket 47: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 47: 30%\n bucket 48: 50%\n bucket 47: 40%\n bucket 48: 60%\n bucket 48: 70%\n bucket 47: 50%\n bucket 48: 80%\n bucket 47: 60%\n bucket 48: 90%\n bucket 47: 70%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\nGetting block 50 of 60\n bucket 49: 90%\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n Sorting block time: 00:00:00\n bucket 50: 100%\nReturning block of 75 for bucket 49\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n Entering block accumulator loop for bucket 51:\n bucket 52: 20%\n bucket 51: 10%\n bucket 52: 30%\n bucket 52: 40%\n bucket 51: 20%\n bucket 52: 50%\n bucket 51: 30%\n bucket 52: 60%\n bucket 51: 40%\n bucket 52: 70%\n bucket 51: 50%\n bucket 52: 80%\n bucket 52: 90%\n bucket 51: 60%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n bucket 53: 20%\n Calculating Z arrays for bucket 54\n bucket 53: 30%\n bucket 53: 40%\n Entering block accumulator loop for bucket 54:\n bucket 53: 50%\n bucket 54: 10%\n bucket 53: 60%\n bucket 54: 20%\n bucket 53: 70%\n bucket 54: 30%\n bucket 53: 80%\n bucket 54: 40%\n bucket 53: 90%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n Entering block accumulator loop for bucket 56:\n bucket 55: 20%\n bucket 56: 10%\n bucket 55: 30%\n bucket 56: 20%\n bucket 55: 40%\n bucket 56: 30%\n bucket 55: 50%\n bucket 56: 40%\n bucket 55: 60%\n bucket 56: 50%\n bucket 55: 70%\n bucket 56: 60%\n bucket 55: 80%\n bucket 56: 70%\n bucket 55: 90%\n bucket 56: 80%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 58:\n Entering block accumulator loop for bucket 59:\n bucket 58: 10%\n bucket 59: 10%\n bucket 58: 20%\n bucket 59: 20%\n bucket 58: 30%\n bucket 59: 30%\n bucket 58: 40%\n bucket 59: 40%\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n bucket 59: 50%\n bucket 58: 50%\n Calculating Z arrays for bucket 60\n bucket 59: 60%\n bucket 58: 60%\n bucket 59: 70%\n Entering block accumulator loop for bucket 60:\n bucket 58: 70%\n bucket 59: 80%\n bucket 60: 10%\n bucket 59: 90%\n bucket 58: 80%\n bucket 60: 20%\n bucket 59: 100%\n bucket 58: 90%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 30%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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", "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 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --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": "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 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 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 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 3 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n Reserving size (126) for bucket 3\nGetting block 4 of 60\n Calculating Z arrays for bucket 3\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 5\n Reserving size (126) for bucket 4\nGetting block 6 of 60\n Entering block accumulator loop for bucket 2:\n bucket 1: 10%\n Reserving size (126) for bucket 6\nGetting block 7 of 60\n Reserving size (126) for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 5:\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 4\n bucket 2: 10%\n Calculating Z arrays for bucket 8\n bucket 1: 20%\n bucket 3: 10%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 7:\n bucket 5: 10%\n Entering block accumulator loop for bucket 8:\n bucket 6: 10%\n bucket 1: 30%\n bucket 7: 10%\n bucket 4: 10%\n bucket 1: 40%\n bucket 6: 20%\n bucket 5: 20%\n bucket 8: 10%\n bucket 4: 20%\n bucket 6: 30%\n bucket 2: 20%\n bucket 7: 20%\n bucket 3: 20%\n bucket 6: 40%\n bucket 8: 20%\n bucket 3: 30%\n bucket 4: 30%\n bucket 6: 50%\n bucket 2: 30%\n bucket 3: 40%\n bucket 1: 50%\n bucket 4: 40%\n bucket 8: 30%\n bucket 6: 60%\n bucket 2: 40%\n bucket 4: 50%\n bucket 5: 30%\n bucket 7: 30%\n bucket 8: 40%\n bucket 1: 60%\n bucket 5: 40%\n bucket 6: 70%\n bucket 3: 50%\n bucket 4: 60%\n bucket 6: 80%\n bucket 8: 50%\n bucket 1: 70%\n bucket 3: 60%\n bucket 6: 90%\n bucket 2: 50%\n bucket 3: 70%\n bucket 1: 80%\n bucket 5: 50%\n bucket 6: 100%\n bucket 7: 40%\n bucket 3: 80%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 4: 70%\n bucket 2: 60%\n bucket 3: 90%\n bucket 1: 90%\n bucket 4: 80%\n bucket 7: 50%\n bucket 5: 60%\n bucket 8: 60%\n bucket 2: 70%\n bucket 7: 60%\n bucket 5: 70%\n bucket 8: 70%\n bucket 4: 90%\n bucket 3: 100%\n bucket 7: 70%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 2: 80%\n bucket 5: 80%\n bucket 4: 100%\n bucket 8: 80%\n bucket 5: 90%\n Sorting block of length 68 for bucket 4\n bucket 2: 90%\n bucket 1: 100%\n bucket 5: 100%\n (Using difference cover)\n bucket 8: 90%\n bucket 2: 100%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Sorting block of length 63 for bucket 5\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n (Using difference cover)\n bucket 8: 100%\n Sorting block time: 00:00:00\n Sorting block of length 94 for bucket 8\n (Using difference cover)\nReturning block of 91 for bucket 6\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\nGetting block 10 of 60\n bucket 9: 10%\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n Entering block accumulator loop for bucket 10:\n bucket 9: 50%\n bucket 10: 10%\n bucket 9: 60%\n bucket 10: 20%\n bucket 9: 70%\n bucket 10: 30%\n bucket 9: 80%\n bucket 10: 40%\n bucket 9: 90%\n bucket 10: 50%\n bucket 10: 60%\n bucket 9: 100%\n Sorting block of length 124 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 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Reserving size (126) 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%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n bucket 12: 20%\n Calculating Z arrays for bucket 13\n bucket 11: 20%\n bucket 12: 30%\n Entering block accumulator loop for bucket 13:\n bucket 11: 30%\n bucket 12: 40%\n bucket 11: 40%\n bucket 13: 10%\n bucket 12: 50%\n bucket 11: 50%\n bucket 13: 20%\n bucket 12: 60%\n bucket 11: 60%\n bucket 13: 30%\n bucket 12: 70%\n bucket 11: 70%\n bucket 12: 80%\n bucket 13: 40%\n bucket 12: 90%\n bucket 13: 50%\n bucket 11: 80%\n bucket 13: 60%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 70%\n bucket 11: 90%\n bucket 13: 80%\n bucket 13: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 14 of 60\n Reserving size (126) 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%\nGetting block 15 of 60\n bucket 14: 70%\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 80%\n bucket 14: 90%\n Entering block accumulator loop for bucket 15:\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\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 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 60\n Reserving size (126) 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 17: 30%\n bucket 16: 60%\n bucket 17: 40%\n bucket 16: 70%\n bucket 17: 50%\n bucket 16: 80%\n bucket 17: 60%\n bucket 16: 90%\n bucket 17: 70%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) 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%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\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 122 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 bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Reserving size (126) for bucket 20\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 20: 30%\n bucket 21: 50%\n bucket 20: 40%\n bucket 21: 60%\n bucket 21: 70%\n bucket 20: 50%\n bucket 21: 80%\n bucket 20: 60%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 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 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) 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 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 80 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\n Reserving size (126) 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%\nGetting block 25 of 60\n bucket 24: 60%\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 70%\n bucket 24: 80%\n Entering block accumulator loop for bucket 25:\n bucket 24: 90%\n bucket 25: 10%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n bucket 25: 20%\n (Using difference cover)\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 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) 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 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) 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 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Entering block accumulator loop for bucket 28:\n Calculating Z arrays for bucket 29\n bucket 28: 10%\n Entering block accumulator loop for bucket 29:\n bucket 28: 20%\n bucket 28: 30%\n bucket 29: 10%\n bucket 28: 40%\n bucket 29: 20%\n bucket 28: 50%\n bucket 29: 30%\n bucket 28: 60%\n bucket 29: 40%\n bucket 28: 70%\n bucket 29: 50%\n bucket 28: 80%\n bucket 29: 60%\n bucket 28: 90%\n bucket 29: 70%\n bucket 28: 100%\n bucket 29: 80%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n Entering block accumulator loop for bucket 31:\n bucket 30: 20%\n bucket 31: 10%\n bucket 30: 30%\n bucket 31: 20%\n bucket 30: 40%\n bucket 31: 30%\n bucket 30: 50%\n bucket 31: 40%\n bucket 30: 60%\n bucket 31: 50%\n bucket 30: 70%\n bucket 31: 60%\n bucket 30: 80%\n bucket 31: 70%\n bucket 30: 90%\n bucket 31: 80%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\n bucket 32: 40%\n bucket 32: 50%\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\nGetting block 35 of 60\n bucket 34: 60%\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 70%\n bucket 34: 80%\n Entering block accumulator loop for bucket 35:\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\nGetting block 37 of 60\n bucket 36: 40%\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 50%\n Entering block accumulator loop for bucket 37:\n bucket 36: 60%\n bucket 37: 10%\n bucket 36: 70%\n bucket 37: 20%\n bucket 36: 80%\n bucket 37: 30%\n bucket 36: 90%\n bucket 37: 40%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n bucket 38: 20%\n Entering block accumulator loop for bucket 39:\n bucket 38: 30%\n bucket 39: 10%\n bucket 38: 40%\n bucket 39: 20%\n bucket 38: 50%\n bucket 39: 30%\n bucket 39: 40%\n bucket 38: 60%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 38: 70%\n bucket 39: 80%\n bucket 38: 80%\n bucket 39: 90%\n bucket 38: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 40:\n bucket 41: 10%\n bucket 40: 10%\n bucket 41: 20%\n bucket 40: 20%\n bucket 41: 30%\n bucket 40: 30%\n bucket 41: 40%\n bucket 40: 40%\n bucket 41: 50%\n bucket 40: 50%\n bucket 41: 60%\n bucket 40: 60%\n bucket 41: 70%\n bucket 40: 70%\n bucket 41: 80%\n bucket 40: 80%\n bucket 41: 90%\n bucket 40: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n bucket 42: 60%\n Calculating Z arrays for bucket 43\n bucket 42: 70%\n bucket 42: 80%\n Entering block accumulator loop for bucket 43:\n bucket 42: 90%\n bucket 42: 100%\n bucket 43: 10%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n Entering block accumulator loop for bucket 45:\n bucket 44: 20%\n bucket 45: 10%\n bucket 44: 30%\n bucket 44: 40%\n bucket 45: 20%\n bucket 44: 50%\n bucket 45: 30%\n bucket 44: 60%\n bucket 44: 70%\n bucket 45: 40%\n bucket 44: 80%\n bucket 45: 50%\n bucket 44: 90%\n bucket 45: 60%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 47:\n Entering block accumulator loop for bucket 48:\n bucket 47: 10%\n bucket 48: 10%\n bucket 48: 20%\n bucket 47: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 47: 30%\n bucket 48: 50%\n bucket 47: 40%\n bucket 48: 60%\n bucket 48: 70%\n bucket 47: 50%\n bucket 48: 80%\n bucket 47: 60%\n bucket 48: 90%\n bucket 47: 70%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\nGetting block 50 of 60\n bucket 49: 90%\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n Sorting block time: 00:00:00\n bucket 50: 100%\nReturning block of 75 for bucket 49\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n Entering block accumulator loop for bucket 51:\n bucket 52: 20%\n bucket 51: 10%\n bucket 52: 30%\n bucket 52: 40%\n bucket 51: 20%\n bucket 52: 50%\n bucket 51: 30%\n bucket 52: 60%\n bucket 51: 40%\n bucket 52: 70%\n bucket 51: 50%\n bucket 52: 80%\n bucket 52: 90%\n bucket 51: 60%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n bucket 53: 20%\n Calculating Z arrays for bucket 54\n bucket 53: 30%\n bucket 53: 40%\n Entering block accumulator loop for bucket 54:\n bucket 53: 50%\n bucket 54: 10%\n bucket 53: 60%\n bucket 54: 20%\n bucket 53: 70%\n bucket 54: 30%\n bucket 53: 80%\n bucket 54: 40%\n bucket 53: 90%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n Entering block accumulator loop for bucket 56:\n bucket 55: 20%\n bucket 56: 10%\n bucket 55: 30%\n bucket 56: 20%\n bucket 55: 40%\n bucket 56: 30%\n bucket 55: 50%\n bucket 56: 40%\n bucket 55: 60%\n bucket 56: 50%\n bucket 55: 70%\n bucket 56: 60%\n bucket 55: 80%\n bucket 56: 70%\n bucket 55: 90%\n bucket 56: 80%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 58:\n Entering block accumulator loop for bucket 59:\n bucket 58: 10%\n bucket 59: 10%\n bucket 58: 20%\n bucket 59: 20%\n bucket 58: 30%\n bucket 59: 30%\n bucket 58: 40%\n bucket 59: 40%\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n bucket 59: 50%\n bucket 58: 50%\n Calculating Z arrays for bucket 60\n bucket 59: 60%\n bucket 58: 60%\n bucket 59: 70%\n Entering block accumulator loop for bucket 60:\n bucket 58: 70%\n bucket 59: 80%\n bucket 60: 10%\n bucket 59: 90%\n bucket 58: 80%\n bucket 60: 20%\n bucket 59: 100%\n bucket 58: 90%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 30%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\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": "2025-01-14 13:38:59", "plugin": "core", "name": "end_epoch", "raw_value": "1736861939.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:38:59", "plugin": "core", "name": "start_epoch", "raw_value": "1736861939.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "ivar_removereads/1.4.3+galaxy0-0", "has_data": true, "data": {"tool_id": "ivar_removereads", "tool_version": "1.4.3+galaxy0", "test_index": 0, "time_seconds": 44.17165994644165, "inputs": {"input_bam": {"src": "hda", "id": "c6c8d129e99d243b"}, "variants_tsv": {"src": "hda", "id": "a44589b18155804b"}, "input_bed": {"src": "hda", "id": "7a0cb9a3e14eb418"}, "amplicons|amplicon_info": {"src": "hda", "id": "68772c242e331cd3"}, "amplicons|computed": "no"}, "job": {"model_class": "Job", "id": "0a715624bfcd70a3", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:32:36.090147", "create_time": "2025-01-14T13:32:17.043436", "galaxy_version": "23.1", "command_version": "iVar version 1.4.3", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-wphbq", "command_line": "cp '/galaxy/server/database/objects/f/e/f/dataset_fefa8cb2-d329-48af-99a4-a8536e69faf5.dat' binding_sites.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/ivar_removereads/sanitize_bed.py' binding_sites.bed && ln -s '/galaxy/server/database/objects/d/3/c/dataset_d3c626e9-c07c-4499-a12b-ef8d89e23d85.dat' amplicon_info.tsv && ivar getmasked -i '/galaxy/server/database/objects/a/1/8/dataset_a18f6fa2-d4a4-4002-bc14-ed1ad8000f67.dat' -b binding_sites.bed -f amplicon_info.tsv -p masked_primers && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/ivar_removereads/completemask.py' masked_primers.txt amplicon_info.tsv && ln -s '/galaxy/server/database/objects/8/5/7/dataset_857a43b7-ffa1-408f-bfed-0af6e11329af.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/e/a/e/metadata_eae7ff50-ae23-4236-b225-afc5e6b02dda.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": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "amplicons": "{\"__current_case__\": 1, \"amplicon_info\": {\"values\": [{\"id\": 189, \"src\": \"hda\"}]}, \"computed\": \"no\"}"}, "inputs": {"input_bam": {"id": "c6c8d129e99d243b", "src": "hda", "uuid": "857a43b7-ffa1-408f-bfed-0af6e11329af"}, "variants_tsv": {"id": "a44589b18155804b", "src": "hda", "uuid": "a18f6fa2-d4a4-4002-bc14-ed1ad8000f67"}, "input_bed": {"id": "7a0cb9a3e14eb418", "src": "hda", "uuid": "fefa8cb2-d329-48af-99a4-a8536e69faf5"}, "amplicons|amplicon_info": {"id": "68772c242e331cd3", "src": "hda", "uuid": "d3c626e9-c07c-4499-a12b-ef8d89e23d85"}}, "outputs": {"output_bam": {"id": "061538777969fbfb", "src": "hda", "uuid": "cbf35c8f-1d89-4f63-be01-0ce62afa5507"}}, "output_collections": {}, "tool_stdout": "400_18_out_L**\n400_23_out_R\n400_32_out_L\n400_18_out_L**\t400_18_out_R**\t400_23_out_R\t400_23_out_L\t400_32_out_L\t400_32_out_R\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\nWriting to removed_reads.bam\nNumber of references: 1\nReference Name: PRV\nReference Length: 10807\nUsing Region: PRV\nSorted By Coordinate\nResults:\n2035 reads were removed.\n", "tool_stderr": "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.\nFound 67 primers in BED file\n", "job_stdout": "", "job_stderr": "", "stderr": "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.\nFound 67 primers in BED file\n", "stdout": "400_18_out_L**\n400_23_out_R\n400_32_out_L\n400_18_out_L**\t400_18_out_R**\t400_23_out_R\t400_23_out_L\t400_32_out_L\t400_32_out_R\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\nWriting to removed_reads.bam\nNumber of references: 1\nReference Name: PRV\nReference Length: 10807\nUsing Region: PRV\nSorted By Coordinate\nResults:\n2035 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": "2025-01-14 13:32:24", "plugin": "core", "name": "end_epoch", "raw_value": "1736861544.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:32:23", "plugin": "core", "name": "start_epoch", "raw_value": "1736861543.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "ivar_removereads/1.4.3+galaxy0-1", "has_data": true, "data": {"tool_id": "ivar_removereads", "tool_version": "1.4.3+galaxy0", "test_index": 1, "time_seconds": 34.63112449645996, "inputs": {"input_bam": {"src": "hda", "id": "5cc31279f2fd62aa"}, "variants_tsv": {"src": "hda", "id": "e1bbba116b2d216c"}, "input_bed": {"src": "hda", "id": "0141e4fd024ad171"}, "amplicons|computed": "yes"}, "job": {"model_class": "Job", "id": "2a9b57c2cff07119", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:33:10.791135", "create_time": "2025-01-14T13:32:59.138764", "galaxy_version": "23.1", "command_version": "iVar version 1.4.3", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-8pz4f", "command_line": "cp '/galaxy/server/database/objects/9/6/a/dataset_96a51647-23fc-49c6-94a7-e68922542907.dat' binding_sites.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/ivar_removereads/sanitize_bed.py' binding_sites.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/ivar_removereads/write_amplicon_info_file.py' binding_sites.bed amplicon_info.tsv && ivar getmasked -i '/galaxy/server/database/objects/6/7/4/dataset_6748c3bf-72b7-4b93-8940-47c4f196eaf1.dat' -b binding_sites.bed -f amplicon_info.tsv -p masked_primers && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/ivar_removereads/completemask.py' masked_primers.txt amplicon_info.tsv && ln -s '/galaxy/server/database/objects/7/8/d/dataset_78de0de9-4755-4678-91a5-e9f03655d2f8.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/c/c/f/metadata_ccf2e97a-8d88-4061-91d8-8f293fe04c25.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": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "amplicons": "{\"__current_case__\": 0, \"computed\": \"yes\"}"}, "inputs": {"input_bam": {"id": "5cc31279f2fd62aa", "src": "hda", "uuid": "78de0de9-4755-4678-91a5-e9f03655d2f8"}, "variants_tsv": {"id": "e1bbba116b2d216c", "src": "hda", "uuid": "6748c3bf-72b7-4b93-8940-47c4f196eaf1"}, "input_bed": {"id": "0141e4fd024ad171", "src": "hda", "uuid": "96a51647-23fc-49c6-94a7-e68922542907"}}, "outputs": {"output_bam": {"id": "34cc711b097cb055", "src": "hda", "uuid": "1a40862a-13c7-4e62-ac98-7bcfa7dfc786"}}, "output_collections": {}, "tool_stdout": "400_18_out_L**\n400_23_out_R\n400_32_out_L\n400_18_out_L**\t400_18_out_R**\t400_23_out_R\t400_23_out_L\t400_32_out_L\t400_32_out_R\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\nWriting to removed_reads.bam\nNumber of references: 1\nReference Name: PRV\nReference Length: 10807\nUsing Region: PRV\nSorted By Coordinate\nResults:\n2035 reads were removed.\n", "tool_stderr": "Found 67 primers in BED file\nPrimer pair is empty.\nPrimer pair is empty.\nPrimer pair is empty.\nFound 67 primers in BED file\n", "job_stdout": "", "job_stderr": "", "stderr": "Found 67 primers in BED file\nPrimer pair is empty.\nPrimer pair is empty.\nPrimer pair is empty.\nFound 67 primers in BED file\n", "stdout": "400_18_out_L**\n400_23_out_R\n400_32_out_L\n400_18_out_L**\t400_18_out_R**\t400_23_out_R\t400_23_out_L\t400_32_out_L\t400_32_out_R\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\nWriting to removed_reads.bam\nNumber of references: 1\nReference Name: PRV\nReference Length: 10807\nUsing Region: PRV\nSorted By Coordinate\nResults:\n2035 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": "2025-01-14 13:33:01", "plugin": "core", "name": "end_epoch", "raw_value": "1736861581.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:33:00", "plugin": "core", "name": "start_epoch", "raw_value": "1736861580.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "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": 50.82345771789551, "inputs": {"input": {"src": "hda", "id": "fcce236af6e81fef"}, "type": "fwd"}, "job": {"model_class": "Job", "id": "c93414dc33079a5c", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:12:03.424546", "create_time": "2025-01-14T13:11:28.666282", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-j7q7d", "command_line": "poretools tabular --type fwd '/galaxy/server/database/objects/3/b/1/dataset_3b117654-62b8-457a-8f7f-3a684bfeff4a.dat' > '/galaxy/server/database/objects/4/6/6/dataset_466afed3-8351-4446-9cff-4c6aff412d1d.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "type": "\"fwd\""}, "inputs": {"input": {"id": "fcce236af6e81fef", "src": "hda", "uuid": "3b117654-62b8-457a-8f7f-3a684bfeff4a"}}, "outputs": {"output": {"id": "19726fcc58dc13f7", "src": "hda", "uuid": "466afed3-8351-4446-9cff-4c6aff412d1d"}}, "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": "2025-01-14 13:11:46", "plugin": "core", "name": "end_epoch", "raw_value": "1736860306.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:11:45", "plugin": "core", "name": "start_epoch", "raw_value": "1736860305.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "poretools_tabular/0.6.1a1.0-1", "has_data": true, "data": {"tool_id": "poretools_tabular", "tool_version": "0.6.1a1.0", "test_index": 1, "time_seconds": 28.227001905441284, "inputs": {"input": {"src": "hda", "id": "e1f2e5f5e923b37e"}, "type": "rev"}, "job": {"model_class": "Job", "id": "cc722ab938a2ed65", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:12:31.827187", "create_time": "2025-01-14T13:12:20.254445", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-qxxjv", "command_line": "poretools tabular --type rev '/galaxy/server/database/objects/0/d/8/dataset_0d8dfe89-8426-45e3-9ade-c1670290d088.dat' > '/galaxy/server/database/objects/5/d/3/dataset_5d3e2a4f-fd1a-4c61-92f3-9105991bc929.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "type": "\"rev\""}, "inputs": {"input": {"id": "e1f2e5f5e923b37e", "src": "hda", "uuid": "0d8dfe89-8426-45e3-9ade-c1670290d088"}}, "outputs": {"output": {"id": "542c6ee25a36c432", "src": "hda", "uuid": "5d3e2a4f-fd1a-4c61-92f3-9105991bc929"}}, "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": "2025-01-14 13:12:22", "plugin": "core", "name": "end_epoch", "raw_value": "1736860342.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:12:22", "plugin": "core", "name": "start_epoch", "raw_value": "1736860342.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "poretools_tabular/0.6.1a1.0-2", "has_data": true, "data": {"tool_id": "poretools_tabular", "tool_version": "0.6.1a1.0", "test_index": 2, "time_seconds": 28.311678647994995, "inputs": {"input": {"src": "hda", "id": "3a573123332b5773"}, "type": "2D"}, "job": {"model_class": "Job", "id": "62492a51c4a525b5", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:13:00.213331", "create_time": "2025-01-14T13:12:49.454350", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-mc4l8", "command_line": "poretools tabular --type 2D '/galaxy/server/database/objects/f/2/b/dataset_f2b7add5-df06-4c7a-9aa6-db0e996ebb2d.dat' > '/galaxy/server/database/objects/5/0/1/dataset_5010ec48-7154-41d2-8ee9-5d346f906e65.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "type": "\"2D\""}, "inputs": {"input": {"id": "3a573123332b5773", "src": "hda", "uuid": "f2b7add5-df06-4c7a-9aa6-db0e996ebb2d"}}, "outputs": {"output": {"id": "251c84d7eaadebc5", "src": "hda", "uuid": "5010ec48-7154-41d2-8ee9-5d346f906e65"}}, "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": "2025-01-14 13:12:51", "plugin": "core", "name": "end_epoch", "raw_value": "1736860371.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:12:50", "plugin": "core", "name": "start_epoch", "raw_value": "1736860370.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "poretools_tabular/0.6.1a1.0-3", "has_data": true, "data": {"tool_id": "poretools_tabular", "tool_version": "0.6.1a1.0", "test_index": 3, "time_seconds": 27.884020566940308, "inputs": {"input": {"src": "hda", "id": "f6d30d7077ef1210"}, "type": "best"}, "job": {"model_class": "Job", "id": "12177588ca8de124", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:13:28.555636", "create_time": "2025-01-14T13:13:17.030739", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0", "history_id": 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'/galaxy/server/database/objects/5/5/a/dataset_55a74742-3600-4262-b5ad-0a627be94910.dat' fq2.fastq && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 -1 'fq1.fastq' -2 'fq2.fastq' --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --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_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2' --keep 0", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "reuse": "[]", "keep": "\"0\"", "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"no_simple_bridges\": false, \"scores\": \"3,-6,-5,-2\"}", "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", "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\"}", "min_anchor_seg_len": "\"\"", "linear_seqs": "\"0\"", "min_fasta_length": "\"100\"", "mode": "\"normal\"", "long": null, "paired_unpaired": "{\"__current_case__\": 0, \"fastq_input1\": {\"values\": [{\"id\": 139, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 140, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"paired\"}"}, "inputs": {"paired_unpaired|fastq_input1": {"id": "1ca81c9948d1e927", "src": "hda", "uuid": "9e81b5fb-101a-462e-becf-750cb0693ad2"}, "paired_unpaired|fastq_input2": {"id": "5d7fc42a2592dec7", "src": "hda", "uuid": "55a74742-3600-4262-b5ad-0a627be94910"}}, "outputs": {"assembly_graph": {"id": "e7a83eb3d4b88a6e", "src": "hda", "uuid": "e79c210c-ea69-4214-9b27-cd7b8be10c15"}, "assembly": {"id": "87da9298709c34f1", "src": "hda", "uuid": "a95dc747-3975-4c0b-8052-c10c0b82fc6f"}}, "output_collections": {}, "tool_stdout": "\nStarting Unicycler (2025-01-14 13:16:08)\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 8 -o ./ --verbosity 3 -1 fq1.fastq -2 fq2.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --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_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 0\n\nUnicycler version: v0.5.1\nUsing 8 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/118/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 4.0.0 good /usr/local/bin/spades.py \n racon not used \n makeblastdb 2.16.0+ good /usr/local/bin/makeblastdb\n tblastn 2.16.0+ good /usr/local/bin/tblastn \n\n\nChoosing k-mer range for assembly (2025-01-14 13:16:08)\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 (2025-01-14 13:16:08)\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\nspades.py -o /galaxy/server/database/jobs_directory/000/118/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/118/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/118/working/fq2.fastq -m 1024\n== Warning == output dir is not empty! Please, clean output directory before run.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/118/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/118/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/118/working/fq2.fastq -m 1024\n\nSystem information:\n SPAdes version: 4.0.0\n Python version: 3.12.4\n OS: Linux-6.1.112+-x86_64-with-glibc2.36\nOutput dir: /galaxy/server/database/jobs_directory/000/118/working/spades_assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Isolate mode\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/118/working/fq1.fastq']\n right reads: ['/galaxy/server/database/jobs_directory/000/118/working/fq2.fastq']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\n Assembly graph output will use GFA v1.1 format\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/tmp\n Threads: 8\n Memory limit (in Gb): 1024\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/spades.log\n/galaxy/server/database/jobs_directory/000/118/working/fq1.fastq: max reads length: 251\n/galaxy/server/database/jobs_directory/000/118/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/000/118/working/spades_assembly/K27/configs/config.info /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K27/configs/isolate_mode.info\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K27/configs/config.info\"\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K27/configs/isolate_mode.info\"\n 0:00:00.000 1M / 20M INFO General (memory_limit.cpp : 55) Memory limit set to 1024 Gb\n 0:00:00.000 1M / 20M INFO General (main.cpp : 102) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 1M / 20M INFO General (main.cpp : 103) Maximum k-mer length: 128\n 0:00:00.000 1M / 20M INFO General (main.cpp : 104) Assembling dataset (\"/galaxy/server/database/jobs_directory/000/118/working/spades_assembly/dataset.info\") with K=27\n 0:00:00.000 1M / 20M INFO General (main.cpp : 105) Maximum # of threads to use (adjusted due to OMP capabilities): 8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 212) SPAdes started\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 234) Two-step repeat resolution disabled\n 0:00:00.001 1M / 20M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3\n 0:00:00.001 1M / 20M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40\n 0:00:00.001 1M / 20M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 245) Will need read mapping, kmer mapper will be attached\n 0:00:00.001 1M / 20M INFO StageManager (stage.cpp : 189) STAGE == Binary Read Conversion (id: read_conversion)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 78) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 99) Converting paired reads\n 0:00:00.069 81M / 81M INFO General (binary_converter.cpp : 143) 7925 reads written\n 0:00:00.072 50M / 50M INFO General (read_converter.cpp : 113) Converting single reads\n 0:00:00.087 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.088 50M / 50M INFO General (read_converter.cpp : 119) Converting merged reads\n 0:00:00.096 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.127 1M / 42M INFO StageManager (stage.cpp : 189) STAGE == de Bruijn graph construction (id: construction)\n 0:00:00.144 1M / 42M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.144 1M / 42M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.144 1M / 42M INFO General (stage.cpp : 121) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)\n 0:00:00.144 1M / 42M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:00.145 1M / 42M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:00.145 1M / 42M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:00.145 1M / 42M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:00.862 1M / 55M INFO General (kmer_splitters.hpp : 134) Used 31700 reads\n 0:00:00.866 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:01.094 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 35249 kmers in total.\n 0:00:01.094 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Extension index construction (id: construction:extension_index_construction)\n 0:00:01.139 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index\n 0:00:01.139 1M / 55M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:01.140 1M / 55M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:01.140 1M / 55M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:01.140 1M / 55M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:01.823 4641M / 4641M INFO General (kmer_splitters.hpp : 197) Processed 35249 kmers\n 0:00:01.823 4641M / 4641M INFO General (kmer_splitters.hpp : 202) Used 35249 kmers.\n 0:00:01.823 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:02.048 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 34510 kmers in total.\n 0:00:02.048 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.105 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 34510 kmers, 86928 bytes occupied (20.1514 bits per kmer).\n 0:00:02.105 1M / 55M INFO General (kmer_index_builder.hpp : 168) Merging final buckets.\n 0:00:02.285 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers\n 0:00:02.297 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished.\n 0:00:02.324 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Condensing graph (id: construction:graph_condensing)\n 0:00:02.328 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths\n 0:00:02.332 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2775 sequences extracted\n 0:00:02.334 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops\n 0:00:02.339 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected\n 0:00:02.339 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges...\n 0:00:02.339 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted\n 0:00:02.339 1M / 55M INFO General (debruijn_graph_constructor: 516) Total 5550 edges to create\n 0:00:02.339 2M / 55M INFO General (debruijn_graph_constructor: 519) Collecting link records\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 521) Ordering link records\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 524) Sorting done\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords...\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 542) Total 2036 vertices to create\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 545) Connecting the graph\n 0:00:02.343 2M / 55M INFO General (stage.cpp : 121) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)\n 0:00:02.343 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.378 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 35249 kmers, 87400 bytes occupied (19.836 bits per kmer).\n 0:00:02.378 2M / 55M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.447 2M / 55M INFO General (construction.cpp : 427) Filling coverage and flanking coverage from PHM\n 0:00:02.449 2M / 55M INFO General (coverage_filling.hpp : 83) Processed 5550 edges\n 0:00:02.517 1M / 55M INFO StageManager (stage.cpp : 189) STAGE == EC Threshold Finding (id: ec_threshold_finder)\n 0:00:02.517 1M / 55M INFO General (kmer_coverage_model.cpp : 182) Kmer coverage valley at: 7\n 0:00:02.517 1M / 55M INFO General (kmer_coverage_model.cpp : 202) K-mer histogram maximum: 695\n 0:00:02.517 1M / 55M INFO General (kmer_coverage_model.cpp : 238) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.517 1M / 55M INFO General (kmer_coverage_model.cpp : 260) Fitting coverage model\n 0:00:02.638 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 2\n 0:00:03.052 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 4\n 0:00:03.671 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 8\n 0:00:04.142 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 16\n 0:00:04.945 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 32\n 0:00:04.945 1M / 55M INFO General (kmer_coverage_model.cpp : 310) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:04.946 1M / 55M INFO General (kmer_coverage_model.cpp : 335) Probability of erroneous kmer at valley: 1\n 0:00:04.946 1M / 55M INFO General (kmer_coverage_model.cpp : 359) Preliminary threshold calculated as: 275\n 0:00:04.946 1M / 55M INFO General (kmer_coverage_model.cpp : 363) Threshold adjusted to: 275\n 0:00:04.946 1M / 55M INFO General (kmer_coverage_model.cpp : 376) Estimated genome size (ignoring repeats): 5132\n 0:00:04.946 1M / 55M INFO General (genomic_info_filler.cpp : 56) Mean coverage was calculated as 671.577\n 0:00:04.946 1M / 55M INFO General (genomic_info_filler.cpp : 71) EC coverage threshold value was calculated as 275\n 0:00:04.946 1M / 55M INFO General (genomic_info_filler.cpp : 72) Trusted kmer low bound: 0\n 0:00:04.946 1M / 55M INFO StageManager (stage.cpp : 189\n..\n : 131) Assembling time: 0 hours 0 minutes 4 seconds\n===== K127 finished.\n===== Copy files started.\n== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/before_rr.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/before_rr.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/final_contigs.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/contigs.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/strain_graph.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/strain_graph.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/scaffolds.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/scaffolds.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/scaffolds.paths /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/scaffolds.paths /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/final_contigs.paths /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/contigs.paths\n===== Copy files finished.\n===== Assembling finished.\n===== Breaking scaffolds started.\n== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/scaffolds.fasta --misc_dir /galaxy/server/database/jobs_directory/000/118/working/spades_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/000/118/working/spades_assembly/contigs.fasta\n * Assembled scaffolds are in /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/scaffolds.fasta\n * Paths in the assembly graph corresponding to the contigs are in /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/contigs.paths\n * Paths in the assembly graph corresponding to the scaffolds are in /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/scaffolds.paths\n * Assembly graph is in /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/assembly_graph.fastg\n * Assembly graph in GFA format is in /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/assembly_graph_with_scaffolds.gfa\n======= SPAdes pipeline finished.\nSPAdes log can be found here: /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/spades.log\nThank you for using SPAdes! If you use it in your research, please cite:\n Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. and Korobeynikov, A., 2020. Using SPAdes de novo assembler. Current protocols in bioinformatics, 70(1), p.e102.\n doi.org/10.1002/cpbi.102\n\n\nInsert size mean: 367.3 bp\nInsert size stdev: 37.3 bp\n\n\nCleaning k27 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k027_assembly_graph.gfa\n\nCleaning k47 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k047_assembly_graph.gfa\n\nCleaning k63 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k063_assembly_graph.gfa\n\nCleaning k77 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k077_assembly_graph.gfa\n\nCleaning k89 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k089_assembly_graph.gfa\n\nCleaning k99 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k099_assembly_graph.gfa\n\nCleaning k107 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k107_assembly_graph.gfa\n\nCleaning k115 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k115_assembly_graph.gfa\n\nCleaning k121 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k121_assembly_graph.gfa\n\nCleaning k127 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k27_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2025-01-14 13:18:22)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 1 1 5,413 5,413 5,413 0 5.00e-01 <-best\n 47 1 1 5,433 5,433 5,433 0 5.00e-01\n 63 1 1 5,449 5,449 5,449 0 5.00e-01\n 77 1 1 5,463 5,463 5,463 0 5.00e-01\n 89 1 1 5,475 5,475 5,475 0 5.00e-01\n 99 1 1 5,485 5,485 5,485 0 5.00e-01\n 107 1 1 5,493 5,493 5,493 0 5.00e-01\n 115 1 1 5,501 5,501 5,501 0 5.00e-01\n 121 1 1 5,507 5,507 5,507 0 5.00e-01\n 127 1 1 5,513 5,513 5,513 0 5.00e-01\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k027.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k047.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k063.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k077.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k089.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k099.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k107.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k115.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k121.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k127.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/\n\n\nDetermining graph multiplicity (2025-01-14 13:18:22)\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\n\nCleaning graph (2025-01-14 13:18:22)\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 13 14\nGraph overlaps removed\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 (2025-01-14 13:18:22)\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 (2025-01-14 13:18:22)\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 (2025-01-14 13:18:22)\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\n\nCleaning up leftover segments (2025-01-14 13:18:22)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2025-01-14 13:18:22)\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\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 (2025-01-14 13:18:22)\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/python3.12/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 (2025-01-14 13:18:31)\nSaving /galaxy/server/database/jobs_directory/000/118/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/118/working/assembly.fasta\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\nStarting Unicycler (2025-01-14 13:16:08)\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 8 -o ./ --verbosity 3 -1 fq1.fastq -2 fq2.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --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_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 0\n\nUnicycler version: v0.5.1\nUsing 8 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/118/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 4.0.0 good /usr/local/bin/spades.py \n racon not used \n makeblastdb 2.16.0+ good /usr/local/bin/makeblastdb\n tblastn 2.16.0+ good /usr/local/bin/tblastn \n\n\nChoosing k-mer range for assembly (2025-01-14 13:16:08)\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 (2025-01-14 13:16:08)\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\nspades.py -o /galaxy/server/database/jobs_directory/000/118/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/118/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/118/working/fq2.fastq -m 1024\n== Warning == output dir is not empty! Please, clean output directory before run.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/118/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/118/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/118/working/fq2.fastq -m 1024\n\nSystem information:\n SPAdes version: 4.0.0\n Python version: 3.12.4\n OS: Linux-6.1.112+-x86_64-with-glibc2.36\nOutput dir: /galaxy/server/database/jobs_directory/000/118/working/spades_assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Isolate mode\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/118/working/fq1.fastq']\n right reads: ['/galaxy/server/database/jobs_directory/000/118/working/fq2.fastq']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\n Assembly graph output will use GFA v1.1 format\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/tmp\n Threads: 8\n Memory limit (in Gb): 1024\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/spades.log\n/galaxy/server/database/jobs_directory/000/118/working/fq1.fastq: max reads length: 251\n/galaxy/server/database/jobs_directory/000/118/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/000/118/working/spades_assembly/K27/configs/config.info /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K27/configs/isolate_mode.info\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K27/configs/config.info\"\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K27/configs/isolate_mode.info\"\n 0:00:00.000 1M / 20M INFO General (memory_limit.cpp : 55) Memory limit set to 1024 Gb\n 0:00:00.000 1M / 20M INFO General (main.cpp : 102) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 1M / 20M INFO General (main.cpp : 103) Maximum k-mer length: 128\n 0:00:00.000 1M / 20M INFO General (main.cpp : 104) Assembling dataset (\"/galaxy/server/database/jobs_directory/000/118/working/spades_assembly/dataset.info\") with K=27\n 0:00:00.000 1M / 20M INFO General (main.cpp : 105) Maximum # of threads to use (adjusted due to OMP capabilities): 8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 212) SPAdes started\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 234) Two-step repeat resolution disabled\n 0:00:00.001 1M / 20M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3\n 0:00:00.001 1M / 20M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40\n 0:00:00.001 1M / 20M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 245) Will need read mapping, kmer mapper will be attached\n 0:00:00.001 1M / 20M INFO StageManager (stage.cpp : 189) STAGE == Binary Read Conversion (id: read_conversion)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 78) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 99) Converting paired reads\n 0:00:00.069 81M / 81M INFO General (binary_converter.cpp : 143) 7925 reads written\n 0:00:00.072 50M / 50M INFO General (read_converter.cpp : 113) Converting single reads\n 0:00:00.087 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.088 50M / 50M INFO General (read_converter.cpp : 119) Converting merged reads\n 0:00:00.096 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.127 1M / 42M INFO StageManager (stage.cpp : 189) STAGE == de Bruijn graph construction (id: construction)\n 0:00:00.144 1M / 42M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.144 1M / 42M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.144 1M / 42M INFO General (stage.cpp : 121) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)\n 0:00:00.144 1M / 42M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:00.145 1M / 42M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:00.145 1M / 42M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:00.145 1M / 42M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:00.862 1M / 55M INFO General (kmer_splitters.hpp : 134) Used 31700 reads\n 0:00:00.866 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:01.094 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 35249 kmers in total.\n 0:00:01.094 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Extension index construction (id: construction:extension_index_construction)\n 0:00:01.139 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index\n 0:00:01.139 1M / 55M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:01.140 1M / 55M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:01.140 1M / 55M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:01.140 1M / 55M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:01.823 4641M / 4641M INFO General (kmer_splitters.hpp : 197) Processed 35249 kmers\n 0:00:01.823 4641M / 4641M INFO General (kmer_splitters.hpp : 202) Used 35249 kmers.\n 0:00:01.823 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:02.048 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 34510 kmers in total.\n 0:00:02.048 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.105 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 34510 kmers, 86928 bytes occupied (20.1514 bits per kmer).\n 0:00:02.105 1M / 55M INFO General (kmer_index_builder.hpp : 168) Merging final buckets.\n 0:00:02.285 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers\n 0:00:02.297 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished.\n 0:00:02.324 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Condensing graph (id: construction:graph_condensing)\n 0:00:02.328 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths\n 0:00:02.332 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2775 sequences extracted\n 0:00:02.334 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops\n 0:00:02.339 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected\n 0:00:02.339 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges...\n 0:00:02.339 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted\n 0:00:02.339 1M / 55M INFO General (debruijn_graph_constructor: 516) Total 5550 edges to create\n 0:00:02.339 2M / 55M INFO General (debruijn_graph_constructor: 519) Collecting link records\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 521) Ordering link records\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 524) Sorting done\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords...\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 542) Total 2036 vertices to create\n 0:00:02.341 2M / 55M INFO General (debruijn_graph_constructor: 545) Connecting the graph\n 0:00:02.343 2M / 55M INFO General (stage.cpp : 121) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)\n 0:00:02.343 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.378 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 35249 kmers, 87400 bytes occupied (19.836 bits per kmer).\n 0:00:02.378 2M / 55M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.447 2M / 55M INFO General (construction.cpp : 427) Filling coverage and flanking coverage from PHM\n 0:00:02.449 2M / 55M INFO General (coverage_filling.hpp : 83) Processed 5550 edges\n 0:00:02.517 1M / 55M INFO StageManager (stage.cpp : 189) STAGE == EC Threshold Finding (id: ec_threshold_finder)\n 0:00:02.517 1M / 55M INFO General (kmer_coverage_model.cpp : 182) Kmer coverage valley at: 7\n 0:00:02.517 1M / 55M INFO General (kmer_coverage_model.cpp : 202) K-mer histogram maximum: 695\n 0:00:02.517 1M / 55M INFO General (kmer_coverage_model.cpp : 238) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.517 1M / 55M INFO General (kmer_coverage_model.cpp : 260) Fitting coverage model\n 0:00:02.638 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 2\n 0:00:03.052 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 4\n 0:00:03.671 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 8\n 0:00:04.142 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 16\n 0:00:04.945 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 32\n 0:00:04.945 1M / 55M INFO General (kmer_coverage_model.cpp : 310) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:04.946 1M / 55M INFO General (kmer_coverage_model.cpp : 335) Probability of erroneous kmer at valley: 1\n 0:00:04.946 1M / 55M INFO General (kmer_coverage_model.cpp : 359) Preliminary threshold calculated as: 275\n 0:00:04.946 1M / 55M INFO General (kmer_coverage_model.cpp : 363) Threshold adjusted to: 275\n 0:00:04.946 1M / 55M INFO General (kmer_coverage_model.cpp : 376) Estimated genome size (ignoring repeats): 5132\n 0:00:04.946 1M / 55M INFO General (genomic_info_filler.cpp : 56) Mean coverage was calculated as 671.577\n 0:00:04.946 1M / 55M INFO General (genomic_info_filler.cpp : 71) EC coverage threshold value was calculated as 275\n 0:00:04.946 1M / 55M INFO General (genomic_info_filler.cpp : 72) Trusted kmer low bound: 0\n 0:00:04.946 1M / 55M INFO StageManager (stage.cpp : 189\n..\n : 131) Assembling time: 0 hours 0 minutes 4 seconds\n===== K127 finished.\n===== Copy files started.\n== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/before_rr.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/before_rr.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/final_contigs.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/contigs.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/strain_graph.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/strain_graph.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/scaffolds.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/scaffolds.fasta /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/scaffolds.paths /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/scaffolds.paths /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/K127/final_contigs.paths /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/contigs.paths\n===== Copy files finished.\n===== Assembling finished.\n===== Breaking scaffolds started.\n== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/scaffolds.fasta --misc_dir /galaxy/server/database/jobs_directory/000/118/working/spades_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/000/118/working/spades_assembly/contigs.fasta\n * Assembled scaffolds are in /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/scaffolds.fasta\n * Paths in the assembly graph corresponding to the contigs are in /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/contigs.paths\n * Paths in the assembly graph corresponding to the scaffolds are in /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/scaffolds.paths\n * Assembly graph is in /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/assembly_graph.fastg\n * Assembly graph in GFA format is in /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/assembly_graph_with_scaffolds.gfa\n======= SPAdes pipeline finished.\nSPAdes log can be found here: /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/spades.log\nThank you for using SPAdes! If you use it in your research, please cite:\n Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. and Korobeynikov, A., 2020. Using SPAdes de novo assembler. Current protocols in bioinformatics, 70(1), p.e102.\n doi.org/10.1002/cpbi.102\n\n\nInsert size mean: 367.3 bp\nInsert size stdev: 37.3 bp\n\n\nCleaning k27 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k027_assembly_graph.gfa\n\nCleaning k47 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k047_assembly_graph.gfa\n\nCleaning k63 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k063_assembly_graph.gfa\n\nCleaning k77 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k077_assembly_graph.gfa\n\nCleaning k89 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k089_assembly_graph.gfa\n\nCleaning k99 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k099_assembly_graph.gfa\n\nCleaning k107 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k107_assembly_graph.gfa\n\nCleaning k115 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k115_assembly_graph.gfa\n\nCleaning k121 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k121_assembly_graph.gfa\n\nCleaning k127 graph\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2025-01-14 13:18:22)\nFilter by read depth (2025-01-14 13:18:22)\nFilter homopolymer loops (2025-01-14 13:18:22)\nMerge all possible (2025-01-14 13:18:22)\nNormalise read depths (2025-01-14 13:18:22)\nRemove zero length segments (2025-01-14 13:18:22)\nSort link order (2025-01-14 13:18:22)\nGraph cleaning finished (2025-01-14 13:18:22)\nSaving /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/k27_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2025-01-14 13:18:22)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 1 1 5,413 5,413 5,413 0 5.00e-01 <-best\n 47 1 1 5,433 5,433 5,433 0 5.00e-01\n 63 1 1 5,449 5,449 5,449 0 5.00e-01\n 77 1 1 5,463 5,463 5,463 0 5.00e-01\n 89 1 1 5,475 5,475 5,475 0 5.00e-01\n 99 1 1 5,485 5,485 5,485 0 5.00e-01\n 107 1 1 5,493 5,493 5,493 0 5.00e-01\n 115 1 1 5,501 5,501 5,501 0 5.00e-01\n 121 1 1 5,507 5,507 5,507 0 5.00e-01\n 127 1 1 5,513 5,513 5,513 0 5.00e-01\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k027.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k047.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k063.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k077.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k089.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k099.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k107.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k115.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k121.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/001_spades_graph_k127.gfa\nDeleting /galaxy/server/database/jobs_directory/000/118/working/spades_assembly/\n\n\nDetermining graph multiplicity (2025-01-14 13:18:22)\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\n\nCleaning graph (2025-01-14 13:18:22)\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 13 14\nGraph overlaps removed\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 (2025-01-14 13:18:22)\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 (2025-01-14 13:18:22)\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 (2025-01-14 13:18:22)\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\n\nCleaning up leftover segments (2025-01-14 13:18:22)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2025-01-14 13:18:22)\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\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 (2025-01-14 13:18:22)\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/python3.12/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 (2025-01-14 13:18:31)\nSaving /galaxy/server/database/jobs_directory/000/118/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/118/working/assembly.fasta\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 minutes", "plugin": "core", "name": "runtime_seconds", "raw_value": "144.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:18:31", "plugin": "core", "name": "end_epoch", "raw_value": "1736860711.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:16:07", "plugin": "core", "name": "start_epoch", "raw_value": "1736860567.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "unicycler/0.5.1+galaxy0-1", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.5.1+galaxy0", "test_index": 1, "time_seconds": 181.7646505832672, "inputs": {"paired_unpaired|fastq_input1": {"src": "hda", "id": "f3923107443fee5a"}, "paired_unpaired|fastq_input2": {"src": "hda", "id": "2dc3b7fc43316258"}, "paired_unpaired|fastq_input_selector": "paired", "long": {"src": "hda", "id": "a97588ab7f345c4a"}, "mode": "normal", "min_fasta_length": "100", "linear_seqs": "0", "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", "graph_clean|min_component_size": "1000", "graph_clean|min_dead_end_size": "1000", "lr_align|scores": "3,-6,-5,-2", "keep": "0"}, "job": {"model_class": "Job", "id": "c699365c328d1506", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:21:42.785847", "create_time": "2025-01-14T13:19:03.106488", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-c6zq9", "command_line": "ln -s '/galaxy/server/database/objects/f/b/6/dataset_fb624f61-ff08-4a28-b136-67e53a554830.dat' fq1.fastq.gz && ln -s '/galaxy/server/database/objects/c/8/e/dataset_c8e5beb7-6b6a-4943-9c92-b1d01cb53715.dat' fq2.fastq.gz && ln -s '/galaxy/server/database/objects/a/e/e/dataset_aeefff25-5992-4012-ab21-c8dfe3ab0c4d.dat' 'lr.fasta' && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 -1 'fq1.fastq.gz' -2 'fq2.fastq.gz' -l lr.fasta --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --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_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2' --keep 0", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "reuse": "[]", "keep": "\"0\"", "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"no_simple_bridges\": false, \"scores\": \"3,-6,-5,-2\"}", "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", "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\"}", "min_anchor_seg_len": "\"\"", "linear_seqs": "\"0\"", "min_fasta_length": "\"100\"", "mode": "\"normal\"", "paired_unpaired": "{\"__current_case__\": 0, \"fastq_input1\": {\"values\": [{\"id\": 143, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 144, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"paired\"}"}, "inputs": {"paired_unpaired|fastq_input2": {"id": "2dc3b7fc43316258", "src": "hda", "uuid": "c8e5beb7-6b6a-4943-9c92-b1d01cb53715"}, "long": {"id": "a97588ab7f345c4a", "src": "hda", "uuid": "aeefff25-5992-4012-ab21-c8dfe3ab0c4d"}, "paired_unpaired|fastq_input1": {"id": "f3923107443fee5a", "src": "hda", "uuid": "fb624f61-ff08-4a28-b136-67e53a554830"}}, "outputs": {"assembly_graph": {"id": "0a715624bfcd70a3", "src": "hda", "uuid": "8e4bff3b-72db-4944-b14a-d41b66e69ba5"}, "assembly": {"id": "f9d771d9ed7f024c", "src": "hda", "uuid": "813f0ac1-ece8-4ea8-b8fc-2fbb32b27d25"}}, "output_collections": {}, "tool_stdout": "\nStarting Unicycler (2025-01-14 13:19:05)\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 8 -o ./ --verbosity 3 -1 fq1.fastq.gz -2 fq2.fastq.gz -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --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_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 0\n\nUnicycler version: v0.5.1\nUsing 8 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/122/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 4.0.0 good /usr/local/bin/spades.py \n racon 1.5.0 good /usr/local/bin/racon \n makeblastdb 2.16.0+ good /usr/local/bin/makeblastdb\n tblastn 2.16.0+ good /usr/local/bin/tblastn \n\n\nChoosing k-mer range for assembly (2025-01-14 13:19:05)\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 (2025-01-14 13:19:05)\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\nspades.py -o /galaxy/server/database/jobs_directory/000/122/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/122/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/122/working/fq2.fastq.gz -m 1024\n== Warning == output dir is not empty! Please, clean output directory before run.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/122/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/122/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/122/working/fq2.fastq.gz -m 1024\n\nSystem information:\n SPAdes version: 4.0.0\n Python version: 3.12.4\n OS: Linux-6.1.112+-x86_64-with-glibc2.36\nOutput dir: /galaxy/server/database/jobs_directory/000/122/working/spades_assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Isolate mode\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/122/working/fq1.fastq.gz']\n right reads: ['/galaxy/server/database/jobs_directory/000/122/working/fq2.fastq.gz']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\n Assembly graph output will use GFA v1.1 format\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/tmp\n Threads: 8\n Memory limit (in Gb): 1024\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/spades.log\n/galaxy/server/database/jobs_directory/000/122/working/fq1.fastq.gz: max reads length: 251\n/galaxy/server/database/jobs_directory/000/122/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/000/122/working/spades_assembly/K27/configs/config.info /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/K27/configs/isolate_mode.info\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/122/working/spades_assembly/K27/configs/config.info\"\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/122/working/spades_assembly/K27/configs/isolate_mode.info\"\n 0:00:00.000 1M / 20M INFO General (memory_limit.cpp : 55) Memory limit set to 1024 Gb\n 0:00:00.000 1M / 20M INFO General (main.cpp : 102) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 1M / 20M INFO General (main.cpp : 103) Maximum k-mer length: 128\n 0:00:00.000 1M / 20M INFO General (main.cpp : 104) Assembling dataset (\"/galaxy/server/database/jobs_directory/000/122/working/spades_assembly/dataset.info\") with K=27\n 0:00:00.000 1M / 20M INFO General (main.cpp : 105) Maximum # of threads to use (adjusted due to OMP capabilities): 8\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 212) SPAdes started\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 234) Two-step repeat resolution disabled\n 0:00:00.000 1M / 20M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3\n 0:00:00.000 1M / 20M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40\n 0:00:00.000 1M / 20M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 245) Will need read mapping, kmer mapper will be attached\n 0:00:00.001 1M / 20M INFO StageManager (stage.cpp : 189) STAGE == Binary Read Conversion (id: read_conversion)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 78) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 99) Converting paired reads\n 0:00:00.074 82M / 82M INFO General (binary_converter.cpp : 143) 7925 reads written\n 0:00:00.077 50M / 50M INFO General (read_converter.cpp : 113) Converting single reads\n 0:00:00.091 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.092 50M / 50M INFO General (read_converter.cpp : 119) Converting merged reads\n 0:00:00.100 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.136 1M / 42M INFO StageManager (stage.cpp : 189) STAGE == de Bruijn graph construction (id: construction)\n 0:00:00.154 1M / 42M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.155 1M / 42M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.155 1M / 42M INFO General (stage.cpp : 121) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)\n 0:00:00.155 1M / 42M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:00.156 1M / 42M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:00.156 1M / 42M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:00.156 1M / 42M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:00.895 1M / 55M INFO General (kmer_splitters.hpp : 134) Used 31700 reads\n 0:00:00.898 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:01.120 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 35249 kmers in total.\n 0:00:01.120 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Extension index construction (id: construction:extension_index_construction)\n 0:00:01.172 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index\n 0:00:01.172 1M / 55M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:01.173 1M / 55M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:01.173 1M / 55M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:01.173 1M / 55M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:01.916 4641M / 4641M INFO General (kmer_splitters.hpp : 197) Processed 35249 kmers\n 0:00:01.916 4641M / 4641M INFO General (kmer_splitters.hpp : 202) Used 35249 kmers.\n 0:00:01.916 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:02.149 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 34510 kmers in total.\n 0:00:02.149 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.203 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 34510 kmers, 86928 bytes occupied (20.1514 bits per kmer).\n 0:00:02.203 1M / 55M INFO General (kmer_index_builder.hpp : 168) Merging final buckets.\n 0:00:02.381 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers\n 0:00:02.395 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished.\n 0:00:02.417 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Condensing graph (id: construction:graph_condensing)\n 0:00:02.421 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths\n 0:00:02.424 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2775 sequences extracted\n 0:00:02.426 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops\n 0:00:02.430 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected\n 0:00:02.431 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges...\n 0:00:02.431 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted\n 0:00:02.431 1M / 55M INFO General (debruijn_graph_constructor: 516) Total 5550 edges to create\n 0:00:02.431 2M / 55M INFO General (debruijn_graph_constructor: 519) Collecting link records\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 521) Ordering link records\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 524) Sorting done\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords...\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 542) Total 2036 vertices to create\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 545) Connecting the graph\n 0:00:02.435 2M / 55M INFO General (stage.cpp : 121) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)\n 0:00:02.435 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.469 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 35249 kmers, 87400 bytes occupied (19.836 bits per kmer).\n 0:00:02.470 2M / 55M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.534 2M / 55M INFO General (construction.cpp : 427) Filling coverage and flanking coverage from PHM\n 0:00:02.536 2M / 55M INFO General (coverage_filling.hpp : 83) Processed 5550 edges\n 0:00:02.602 1M / 55M INFO StageManager (stage.cpp : 189) STAGE == EC Threshold Finding (id: ec_threshold_finder)\n 0:00:02.603 1M / 55M INFO General (kmer_coverage_model.cpp : 182) Kmer coverage valley at: 7\n 0:00:02.603 1M / 55M INFO General (kmer_coverage_model.cpp : 202) K-mer histogram maximum: 695\n 0:00:02.603 1M / 55M INFO General (kmer_coverage_model.cpp : 238) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.603 1M / 55M INFO General (kmer_coverage_model.cpp : 260) Fitting coverage model\n 0:00:02.723 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 2\n 0:00:03.138 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 4\n 0:00:03.755 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 8\n 0:00:04.221 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 16\n 0:00:05.018 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 32\n 0:00:05.018 1M / 55M INFO General (kmer_coverage_model.cpp : 310) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:05.019 1M / 55M INFO General (kmer_coverage_model.cpp : 335) Probability of erroneous kmer at valley: 1\n 0:00:05.019 1M / 55M INFO General (kmer_coverage_model.cpp : 359) Preliminary threshold calculated as: 275\n 0:00:05.019 1M / 55M INFO General (kmer_coverage_model.cpp : 363) Threshold adjusted to: 275\n 0:00:05.019 1M / 55M INFO General (kmer_coverage_model.cpp : 376) Estimated genome size (ignoring repeats): 5132\n 0:00:05.019 1M / 55M INFO General (genomic_info_filler.cpp : 56) Mean coverage was calculated as 671.577\n 0:00:05.019 1M / 55M INFO General (genomic_info_filler.cpp : 71) EC coverage threshold value was calculated as 275\n 0:00:05.019 1M / 55M INFO General (genomic_info_filler.cpp : 72) Trusted kmer low bound: 0\n 0:00:05.019 1M / 55M INFO StageManager (stage.cpp \n..\n21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k077_assembly_graph.gfa\n\nCleaning k89 graph\nRepair multi way junctions (2025-01-14 13:21:21)\nFilter by read depth (2025-01-14 13:21:21)\nFilter homopolymer loops (2025-01-14 13:21:21)\nMerge all possible (2025-01-14 13:21:21)\nNormalise read depths (2025-01-14 13:21:21)\nRemove zero length segments (2025-01-14 13:21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k089_assembly_graph.gfa\n\nCleaning k99 graph\nRepair multi way junctions (2025-01-14 13:21:21)\nFilter by read depth (2025-01-14 13:21:21)\nFilter homopolymer loops (2025-01-14 13:21:21)\nMerge all possible (2025-01-14 13:21:21)\nNormalise read depths (2025-01-14 13:21:21)\nRemove zero length segments (2025-01-14 13:21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k099_assembly_graph.gfa\n\nCleaning k107 graph\nRepair multi way junctions (2025-01-14 13:21:21)\nFilter by read depth (2025-01-14 13:21:21)\nFilter homopolymer loops (2025-01-14 13:21:21)\nMerge all possible (2025-01-14 13:21:21)\nNormalise read depths (2025-01-14 13:21:21)\nRemove zero length segments (2025-01-14 13:21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k107_assembly_graph.gfa\n\nCleaning k115 graph\nRepair multi way junctions (2025-01-14 13:21:21)\nFilter by read depth (2025-01-14 13:21:21)\nFilter homopolymer loops (2025-01-14 13:21:21)\nMerge all possible (2025-01-14 13:21:21)\nNormalise read depths (2025-01-14 13:21:21)\nRemove zero length segments (2025-01-14 13:21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k115_assembly_graph.gfa\n\nCleaning k121 graph\nRepair multi way junctions (2025-01-14 13:21:21)\nFilter by read depth (2025-01-14 13:21:21)\nFilter homopolymer loops (2025-01-14 13:21:21)\nMerge all possible (2025-01-14 13:21:21)\nNormalise read depths (2025-01-14 13:21:21)\nRemove zero length segments (2025-01-14 13:21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k121_assembly_graph.gfa\n\nCleaning k127 graph\nRepair multi way junctions (2025-01-14 13:21:22)\nFilter by read depth (2025-01-14 13:21:22)\nFilter homopolymer loops (2025-01-14 13:21:22)\nMerge all possible (2025-01-14 13:21:22)\nNormalise read depths (2025-01-14 13:21:22)\nRemove zero length segments (2025-01-14 13:21:22)\nSort link order (2025-01-14 13:21:22)\nGraph cleaning finished (2025-01-14 13:21:22)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2025-01-14 13:21:22)\nFilter by read depth (2025-01-14 13:21:22)\nFilter homopolymer loops (2025-01-14 13:21:22)\nMerge all possible (2025-01-14 13:21:22)\nNormalise read depths (2025-01-14 13:21:22)\nRemove zero length segments (2025-01-14 13:21:22)\nSort link order (2025-01-14 13:21:22)\nGraph cleaning finished (2025-01-14 13:21:22)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k27_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2025-01-14 13:21:22)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 1 1 5,413 5,413 5,413 0 5.00e-01 <-best\n 47 1 1 5,433 5,433 5,433 0 5.00e-01\n 63 1 1 5,449 5,449 5,449 0 5.00e-01\n 77 1 1 5,463 5,463 5,463 0 5.00e-01\n 89 1 1 5,475 5,475 5,475 0 5.00e-01\n 99 1 1 5,485 5,485 5,485 0 5.00e-01\n 107 1 1 5,493 5,493 5,493 0 5.00e-01\n 115 1 1 5,501 5,501 5,501 0 5.00e-01\n 121 1 1 5,507 5,507 5,507 0 5.00e-01\n 127 1 1 5,513 5,513 5,513 0 5.00e-01\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k027.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k047.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k063.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k077.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k089.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k099.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k107.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k115.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k121.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k127.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/\n\n\nDetermining graph multiplicity (2025-01-14 13:21:22)\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\n\nCleaning graph (2025-01-14 13:21:22)\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 13 14\nGraph overlaps removed\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 (2025-01-14 13:21:22)\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 (2025-01-14 13:21:22)\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 (2025-01-14 13:21:22)\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 (2025-01-14 13:21:22)\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/000/122/working/miniasm_assembly/all_segments.fasta\n1\t5386\t3\t5158\t+\t1\t5386\t227\t5382\t5155\t5155\t255\tcm:i:1149\n1\t5386\t5163\t5383\t+\t1\t5386\t1\t221\t220\t220\t255\tcm:i:47\nNumber of minimap alignments: 1\n\nSaving to /galaxy/server/database/jobs_directory/000/122/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 (2025-01-14 13:21:22)\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/000/122/working/simple_bridging/all_segments.fasta\n1\t5386\t3\t5158\t+\t1\t5386\t227\t5382\t5155\t5155\t255\tcm:i:1149\n1\t5386\t5163\t5383\t+\t1\t5386\t1\t221\t220\t220\t255\tcm:i:47\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 (2025-01-14 13:21:22)\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 (2025-01-14 13:21:22)\n1\t5386\t5\t5161\t+\t1\t5386\t229\t5385\t5156\t5156\t255\tcm:i:959\n1\t5386\t5168\t5384\t+\t1\t5386\t6\t222\t216\t216\t255\tcm:i:39\n\nDone! 1 out of 1 reads aligned\n\n\nAligning reads (2025-01-14 13:21:22)\n1/1: 1 (5386 bp)\nminimap alignments:\n 5,5161,+,1,229,5385\n 5168,5384,+,1,6,222\nReference ranges:\n 1+: 0 - 5386\nRange: 1: 0 - 5386\n common 10-mers: 5464\n line 1: 215 points, score=213.009259 (good)\n line 2: 5153 points, score=5151.000388 (good)\nAll Seqan alignments (time to align = 0.058 s):\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 0 224 5162 5386 + 672 100.00 100.00%\n 1 224 5386 0 5162 + 15486 100.00 100.00%\nFinal alignments:\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 224 5386 0 5162 + 15486 100.00 100.00%\n 1 0 224 5162 5386 + 672 100.00 100.00%\n\n\nRead alignment summary (2025-01-14 13:21:22)\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/000/122/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 (2025-01-14 13:21:22)\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 (2025-01-14 13:21:22)\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\n\nCleaning up leftover segments (2025-01-14 13:21:22)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2025-01-14 13:21:22)\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\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 (2025-01-14 13:21:22)\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/python3.12/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 (2025-01-14 13:21:31)\nSaving /galaxy/server/database/jobs_directory/000/122/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/122/working/assembly.fasta\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\nStarting Unicycler (2025-01-14 13:19:05)\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 8 -o ./ --verbosity 3 -1 fq1.fastq.gz -2 fq2.fastq.gz -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --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_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 0\n\nUnicycler version: v0.5.1\nUsing 8 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/122/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 4.0.0 good /usr/local/bin/spades.py \n racon 1.5.0 good /usr/local/bin/racon \n makeblastdb 2.16.0+ good /usr/local/bin/makeblastdb\n tblastn 2.16.0+ good /usr/local/bin/tblastn \n\n\nChoosing k-mer range for assembly (2025-01-14 13:19:05)\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 (2025-01-14 13:19:05)\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\nspades.py -o /galaxy/server/database/jobs_directory/000/122/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/122/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/122/working/fq2.fastq.gz -m 1024\n== Warning == output dir is not empty! Please, clean output directory before run.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/122/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/122/working/fq1.fastq.gz -2 /galaxy/server/database/jobs_directory/000/122/working/fq2.fastq.gz -m 1024\n\nSystem information:\n SPAdes version: 4.0.0\n Python version: 3.12.4\n OS: Linux-6.1.112+-x86_64-with-glibc2.36\nOutput dir: /galaxy/server/database/jobs_directory/000/122/working/spades_assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Isolate mode\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/122/working/fq1.fastq.gz']\n right reads: ['/galaxy/server/database/jobs_directory/000/122/working/fq2.fastq.gz']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\n Assembly graph output will use GFA v1.1 format\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/tmp\n Threads: 8\n Memory limit (in Gb): 1024\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/spades.log\n/galaxy/server/database/jobs_directory/000/122/working/fq1.fastq.gz: max reads length: 251\n/galaxy/server/database/jobs_directory/000/122/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/000/122/working/spades_assembly/K27/configs/config.info /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/K27/configs/isolate_mode.info\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/122/working/spades_assembly/K27/configs/config.info\"\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/122/working/spades_assembly/K27/configs/isolate_mode.info\"\n 0:00:00.000 1M / 20M INFO General (memory_limit.cpp : 55) Memory limit set to 1024 Gb\n 0:00:00.000 1M / 20M INFO General (main.cpp : 102) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 1M / 20M INFO General (main.cpp : 103) Maximum k-mer length: 128\n 0:00:00.000 1M / 20M INFO General (main.cpp : 104) Assembling dataset (\"/galaxy/server/database/jobs_directory/000/122/working/spades_assembly/dataset.info\") with K=27\n 0:00:00.000 1M / 20M INFO General (main.cpp : 105) Maximum # of threads to use (adjusted due to OMP capabilities): 8\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 212) SPAdes started\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 234) Two-step repeat resolution disabled\n 0:00:00.000 1M / 20M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3\n 0:00:00.000 1M / 20M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40\n 0:00:00.000 1M / 20M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 245) Will need read mapping, kmer mapper will be attached\n 0:00:00.001 1M / 20M INFO StageManager (stage.cpp : 189) STAGE == Binary Read Conversion (id: read_conversion)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 78) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 99) Converting paired reads\n 0:00:00.074 82M / 82M INFO General (binary_converter.cpp : 143) 7925 reads written\n 0:00:00.077 50M / 50M INFO General (read_converter.cpp : 113) Converting single reads\n 0:00:00.091 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.092 50M / 50M INFO General (read_converter.cpp : 119) Converting merged reads\n 0:00:00.100 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.136 1M / 42M INFO StageManager (stage.cpp : 189) STAGE == de Bruijn graph construction (id: construction)\n 0:00:00.154 1M / 42M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.155 1M / 42M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.155 1M / 42M INFO General (stage.cpp : 121) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)\n 0:00:00.155 1M / 42M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:00.156 1M / 42M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:00.156 1M / 42M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:00.156 1M / 42M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:00.895 1M / 55M INFO General (kmer_splitters.hpp : 134) Used 31700 reads\n 0:00:00.898 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:01.120 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 35249 kmers in total.\n 0:00:01.120 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Extension index construction (id: construction:extension_index_construction)\n 0:00:01.172 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index\n 0:00:01.172 1M / 55M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:01.173 1M / 55M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:01.173 1M / 55M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:01.173 1M / 55M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:01.916 4641M / 4641M INFO General (kmer_splitters.hpp : 197) Processed 35249 kmers\n 0:00:01.916 4641M / 4641M INFO General (kmer_splitters.hpp : 202) Used 35249 kmers.\n 0:00:01.916 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:02.149 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 34510 kmers in total.\n 0:00:02.149 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.203 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 34510 kmers, 86928 bytes occupied (20.1514 bits per kmer).\n 0:00:02.203 1M / 55M INFO General (kmer_index_builder.hpp : 168) Merging final buckets.\n 0:00:02.381 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers\n 0:00:02.395 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished.\n 0:00:02.417 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Condensing graph (id: construction:graph_condensing)\n 0:00:02.421 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths\n 0:00:02.424 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2775 sequences extracted\n 0:00:02.426 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops\n 0:00:02.430 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected\n 0:00:02.431 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges...\n 0:00:02.431 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted\n 0:00:02.431 1M / 55M INFO General (debruijn_graph_constructor: 516) Total 5550 edges to create\n 0:00:02.431 2M / 55M INFO General (debruijn_graph_constructor: 519) Collecting link records\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 521) Ordering link records\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 524) Sorting done\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords...\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 542) Total 2036 vertices to create\n 0:00:02.433 2M / 55M INFO General (debruijn_graph_constructor: 545) Connecting the graph\n 0:00:02.435 2M / 55M INFO General (stage.cpp : 121) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)\n 0:00:02.435 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.469 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 35249 kmers, 87400 bytes occupied (19.836 bits per kmer).\n 0:00:02.470 2M / 55M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.534 2M / 55M INFO General (construction.cpp : 427) Filling coverage and flanking coverage from PHM\n 0:00:02.536 2M / 55M INFO General (coverage_filling.hpp : 83) Processed 5550 edges\n 0:00:02.602 1M / 55M INFO StageManager (stage.cpp : 189) STAGE == EC Threshold Finding (id: ec_threshold_finder)\n 0:00:02.603 1M / 55M INFO General (kmer_coverage_model.cpp : 182) Kmer coverage valley at: 7\n 0:00:02.603 1M / 55M INFO General (kmer_coverage_model.cpp : 202) K-mer histogram maximum: 695\n 0:00:02.603 1M / 55M INFO General (kmer_coverage_model.cpp : 238) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.603 1M / 55M INFO General (kmer_coverage_model.cpp : 260) Fitting coverage model\n 0:00:02.723 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 2\n 0:00:03.138 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 4\n 0:00:03.755 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 8\n 0:00:04.221 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 16\n 0:00:05.018 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 32\n 0:00:05.018 1M / 55M INFO General (kmer_coverage_model.cpp : 310) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:05.019 1M / 55M INFO General (kmer_coverage_model.cpp : 335) Probability of erroneous kmer at valley: 1\n 0:00:05.019 1M / 55M INFO General (kmer_coverage_model.cpp : 359) Preliminary threshold calculated as: 275\n 0:00:05.019 1M / 55M INFO General (kmer_coverage_model.cpp : 363) Threshold adjusted to: 275\n 0:00:05.019 1M / 55M INFO General (kmer_coverage_model.cpp : 376) Estimated genome size (ignoring repeats): 5132\n 0:00:05.019 1M / 55M INFO General (genomic_info_filler.cpp : 56) Mean coverage was calculated as 671.577\n 0:00:05.019 1M / 55M INFO General (genomic_info_filler.cpp : 71) EC coverage threshold value was calculated as 275\n 0:00:05.019 1M / 55M INFO General (genomic_info_filler.cpp : 72) Trusted kmer low bound: 0\n 0:00:05.019 1M / 55M INFO StageManager (stage.cpp \n..\n21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k077_assembly_graph.gfa\n\nCleaning k89 graph\nRepair multi way junctions (2025-01-14 13:21:21)\nFilter by read depth (2025-01-14 13:21:21)\nFilter homopolymer loops (2025-01-14 13:21:21)\nMerge all possible (2025-01-14 13:21:21)\nNormalise read depths (2025-01-14 13:21:21)\nRemove zero length segments (2025-01-14 13:21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k089_assembly_graph.gfa\n\nCleaning k99 graph\nRepair multi way junctions (2025-01-14 13:21:21)\nFilter by read depth (2025-01-14 13:21:21)\nFilter homopolymer loops (2025-01-14 13:21:21)\nMerge all possible (2025-01-14 13:21:21)\nNormalise read depths (2025-01-14 13:21:21)\nRemove zero length segments (2025-01-14 13:21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k099_assembly_graph.gfa\n\nCleaning k107 graph\nRepair multi way junctions (2025-01-14 13:21:21)\nFilter by read depth (2025-01-14 13:21:21)\nFilter homopolymer loops (2025-01-14 13:21:21)\nMerge all possible (2025-01-14 13:21:21)\nNormalise read depths (2025-01-14 13:21:21)\nRemove zero length segments (2025-01-14 13:21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k107_assembly_graph.gfa\n\nCleaning k115 graph\nRepair multi way junctions (2025-01-14 13:21:21)\nFilter by read depth (2025-01-14 13:21:21)\nFilter homopolymer loops (2025-01-14 13:21:21)\nMerge all possible (2025-01-14 13:21:21)\nNormalise read depths (2025-01-14 13:21:21)\nRemove zero length segments (2025-01-14 13:21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k115_assembly_graph.gfa\n\nCleaning k121 graph\nRepair multi way junctions (2025-01-14 13:21:21)\nFilter by read depth (2025-01-14 13:21:21)\nFilter homopolymer loops (2025-01-14 13:21:21)\nMerge all possible (2025-01-14 13:21:21)\nNormalise read depths (2025-01-14 13:21:21)\nRemove zero length segments (2025-01-14 13:21:21)\nSort link order (2025-01-14 13:21:21)\nGraph cleaning finished (2025-01-14 13:21:21)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k121_assembly_graph.gfa\n\nCleaning k127 graph\nRepair multi way junctions (2025-01-14 13:21:22)\nFilter by read depth (2025-01-14 13:21:22)\nFilter homopolymer loops (2025-01-14 13:21:22)\nMerge all possible (2025-01-14 13:21:22)\nNormalise read depths (2025-01-14 13:21:22)\nRemove zero length segments (2025-01-14 13:21:22)\nSort link order (2025-01-14 13:21:22)\nGraph cleaning finished (2025-01-14 13:21:22)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2025-01-14 13:21:22)\nFilter by read depth (2025-01-14 13:21:22)\nFilter homopolymer loops (2025-01-14 13:21:22)\nMerge all possible (2025-01-14 13:21:22)\nNormalise read depths (2025-01-14 13:21:22)\nRemove zero length segments (2025-01-14 13:21:22)\nSort link order (2025-01-14 13:21:22)\nGraph cleaning finished (2025-01-14 13:21:22)\nSaving /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/k27_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2025-01-14 13:21:22)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 1 1 5,413 5,413 5,413 0 5.00e-01 <-best\n 47 1 1 5,433 5,433 5,433 0 5.00e-01\n 63 1 1 5,449 5,449 5,449 0 5.00e-01\n 77 1 1 5,463 5,463 5,463 0 5.00e-01\n 89 1 1 5,475 5,475 5,475 0 5.00e-01\n 99 1 1 5,485 5,485 5,485 0 5.00e-01\n 107 1 1 5,493 5,493 5,493 0 5.00e-01\n 115 1 1 5,501 5,501 5,501 0 5.00e-01\n 121 1 1 5,507 5,507 5,507 0 5.00e-01\n 127 1 1 5,513 5,513 5,513 0 5.00e-01\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k027.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k047.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k063.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k077.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k089.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k099.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k107.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k115.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k121.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/001_spades_graph_k127.gfa\nDeleting /galaxy/server/database/jobs_directory/000/122/working/spades_assembly/\n\n\nDetermining graph multiplicity (2025-01-14 13:21:22)\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\n\nCleaning graph (2025-01-14 13:21:22)\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 13 14\nGraph overlaps removed\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 (2025-01-14 13:21:22)\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 (2025-01-14 13:21:22)\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 (2025-01-14 13:21:22)\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 (2025-01-14 13:21:22)\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/000/122/working/miniasm_assembly/all_segments.fasta\n1\t5386\t3\t5158\t+\t1\t5386\t227\t5382\t5155\t5155\t255\tcm:i:1149\n1\t5386\t5163\t5383\t+\t1\t5386\t1\t221\t220\t220\t255\tcm:i:47\nNumber of minimap alignments: 1\n\nSaving to /galaxy/server/database/jobs_directory/000/122/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 (2025-01-14 13:21:22)\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/000/122/working/simple_bridging/all_segments.fasta\n1\t5386\t3\t5158\t+\t1\t5386\t227\t5382\t5155\t5155\t255\tcm:i:1149\n1\t5386\t5163\t5383\t+\t1\t5386\t1\t221\t220\t220\t255\tcm:i:47\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 (2025-01-14 13:21:22)\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 (2025-01-14 13:21:22)\n1\t5386\t5\t5161\t+\t1\t5386\t229\t5385\t5156\t5156\t255\tcm:i:959\n1\t5386\t5168\t5384\t+\t1\t5386\t6\t222\t216\t216\t255\tcm:i:39\n\nDone! 1 out of 1 reads aligned\n\n\nAligning reads (2025-01-14 13:21:22)\n1/1: 1 (5386 bp)\nminimap alignments:\n 5,5161,+,1,229,5385\n 5168,5384,+,1,6,222\nReference ranges:\n 1+: 0 - 5386\nRange: 1: 0 - 5386\n common 10-mers: 5464\n line 1: 215 points, score=213.009259 (good)\n line 2: 5153 points, score=5151.000388 (good)\nAll Seqan alignments (time to align = 0.058 s):\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 0 224 5162 5386 + 672 100.00 100.00%\n 1 224 5386 0 5162 + 15486 100.00 100.00%\nFinal alignments:\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 224 5386 0 5162 + 15486 100.00 100.00%\n 1 0 224 5162 5386 + 672 100.00 100.00%\n\n\nRead alignment summary (2025-01-14 13:21:22)\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/000/122/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 (2025-01-14 13:21:22)\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 (2025-01-14 13:21:22)\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\n\nCleaning up leftover segments (2025-01-14 13:21:22)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2025-01-14 13:21:22)\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\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 (2025-01-14 13:21:22)\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/python3.12/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 (2025-01-14 13:21:31)\nSaving /galaxy/server/database/jobs_directory/000/122/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/122/working/assembly.fasta\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 minutes", "plugin": "core", "name": "runtime_seconds", "raw_value": "146.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:21:31", "plugin": "core", "name": "end_epoch", "raw_value": "1736860891.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:19:05", "plugin": "core", "name": "start_epoch", "raw_value": "1736860745.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "unicycler/0.5.1+galaxy0-2", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.5.1+galaxy0", "test_index": 2, "time_seconds": 18.790519952774048, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "unicycler/0.5.1+galaxy0-3", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.5.1+galaxy0", "test_index": 3, "time_seconds": 29.045434951782227, "inputs": {"paired_unpaired|fastq_input_selector": "none", "long": {"src": "hda", "id": "2a9b57c2cff07119"}, "min_anchor_seg_len": "10", "spades|kmers": "21,23", "keep": "0"}, "job": {"model_class": "Job", "id": "e1f2e5f5e923b37e", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:22:31.049720", "create_time": "2025-01-14T13:22:19.110815", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-zfc6r", "command_line": "ln -s '/galaxy/server/database/objects/a/d/9/dataset_ad9ceb5e-8874-4dff-b1bc-8eca3dd66a80.dat' 'lr.fasta' && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 -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_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2' --keep 0", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "reuse": "[]", "keep": "\"0\"", "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"no_simple_bridges\": false, \"scores\": \"3,-6,-5,-2\"}", "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", "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\"}", "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": "2a9b57c2cff07119", "src": "hda", "uuid": "ad9ceb5e-8874-4dff-b1bc-8eca3dd66a80"}}, "outputs": {"assembly_graph": {"id": "7cedf2ce3d2a3a0a", "src": "hda", "uuid": "5e726445-be45-437f-a5d4-3d9c4706f491"}, "assembly": {"id": "b07111c8f6d74e71", "src": "hda", "uuid": "36f032f6-93e5-4222-86d5-f53efd31a1c0"}}, "output_collections": {}, "tool_stdout": "\nStarting Unicycler (2025-01-14 13:22:21)\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 8 -o ./ --verbosity 3 -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_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 0\n\nUnicycler version: v0.5.1\nUsing 8 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/126/working\n\nDependencies:\n Program Version Status Path \n spades.py not used \n racon 1.5.0 good /usr/local/bin/racon \n makeblastdb 2.16.0+ good /usr/local/bin/makeblastdb\n tblastn 2.16.0+ good /usr/local/bin/tblastn \n\n\nLoading reads (2025-01-14 13:22:21)\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 (2025-01-14 13:22:21)\nSaving to /galaxy/server/database/jobs_directory/000/126/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/000/126/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/000/126/working/miniasm_assembly/12_unitig_graph.gfa\n\n\nPolishing miniasm assembly with Racon (2025-01-14 13:22:21)\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/000/126/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 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/000/126/working/miniasm_assembly/racon_polish/016_rotated.fasta\nSaving /galaxy/server/database/jobs_directory/000/126/working/miniasm_assembly/13_racon_polished.gfa\n\n\nAssembly complete (2025-01-14 13:22:22)\nSaving /galaxy/server/database/jobs_directory/000/126/working/assembly.gfa\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\nStarting Unicycler (2025-01-14 13:22:21)\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 8 -o ./ --verbosity 3 -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_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 0\n\nUnicycler version: v0.5.1\nUsing 8 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/126/working\n\nDependencies:\n Program Version Status Path \n spades.py not used \n racon 1.5.0 good /usr/local/bin/racon \n makeblastdb 2.16.0+ good /usr/local/bin/makeblastdb\n tblastn 2.16.0+ good /usr/local/bin/tblastn \n\n\nLoading reads (2025-01-14 13:22:21)\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 (2025-01-14 13:22:21)\nSaving to /galaxy/server/database/jobs_directory/000/126/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/000/126/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/000/126/working/miniasm_assembly/12_unitig_graph.gfa\n\n\nPolishing miniasm assembly with Racon (2025-01-14 13:22:21)\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/000/126/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/000/126/working/miniasm_assembly/racon_polish/016_rotated.fasta\nSaving /galaxy/server/database/jobs_directory/000/126/working/miniasm_assembly/13_racon_polished.gfa\n\n\nAssembly complete (2025-01-14 13:22:22)\nSaving /galaxy/server/database/jobs_directory/000/126/working/assembly.gfa\n\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": "2025-01-14 13:22:22", "plugin": "core", "name": "end_epoch", "raw_value": "1736860942.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:22:21", "plugin": "core", "name": "start_epoch", "raw_value": "1736860941.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "unicycler/0.5.1+galaxy0-4", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.5.1+galaxy0", "test_index": 4, "time_seconds": 20.564557552337646, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "unicycler/0.5.1+galaxy0-5", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.5.1+galaxy0", "test_index": 5, "time_seconds": 180.83048820495605, "inputs": {"paired_unpaired|fastq_input1": {"src": "hda", "id": "138b009b9f153ab8"}, "paired_unpaired|fastq_input2": {"src": "hda", "id": "cff54bd4b52f88a2"}, "paired_unpaired|fastq_input_selector": "paired", "mode": "normal", "keep": "1"}, "job": {"model_class": "Job", "id": "42ef668ba1dfd3a7", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:25:52.113429", "create_time": "2025-01-14T13:23:11.163034", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-lxzbw", "command_line": "ln -s '/galaxy/server/database/objects/d/9/4/dataset_d9424466-1b97-4b79-b638-f074796966f8.dat' fq1.fastq && ln -s '/galaxy/server/database/objects/c/e/5/dataset_ce5fd9d7-d035-42f5-9236-1d1837c549ca.dat' fq2.fastq && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 -1 'fq1.fastq' -2 'fq2.fastq' --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --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_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2' --keep 1 && mkdir 'spades_graphs' && mv 00*gfa './spades_graphs/'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "reuse": "[]", "keep": "\"1\"", "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"no_simple_bridges\": false, \"scores\": \"3,-6,-5,-2\"}", "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", "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\"}", "min_anchor_seg_len": "\"\"", "linear_seqs": "\"0\"", "min_fasta_length": "\"100\"", "mode": "\"normal\"", "long": null, "paired_unpaired": "{\"__current_case__\": 0, \"fastq_input1\": {\"values\": [{\"id\": 157, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 158, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"paired\"}"}, "inputs": {"paired_unpaired|fastq_input1": {"id": "138b009b9f153ab8", "src": "hda", "uuid": "d9424466-1b97-4b79-b638-f074796966f8"}, "paired_unpaired|fastq_input2": {"id": "cff54bd4b52f88a2", "src": "hda", "uuid": "ce5fd9d7-d035-42f5-9236-1d1837c549ca"}}, "outputs": {"assembly_graph": {"id": "c99d2083a9006619", "src": "hda", "uuid": "c1d14451-1f22-4956-a5d6-8f6c7d93073c"}, "assembly": {"id": "3fc409d6698ea447", "src": "hda", "uuid": "22f65e4a-1c42-4904-b0aa-167ba6ac7894"}, "__new_primary_file_spades_collection|001_spades_graph_k027__": {"id": "1058bf491e452b34", "src": "hda", "uuid": "7845ca4a-ce59-44ca-b527-b3458d1fe9ff"}, "__new_primary_file_spades_collection|001_spades_graph_k047__": {"id": "276cb955b216f6fa", "src": "hda", "uuid": "e1c549e3-8106-4c2d-8549-efaa4955ea7a"}, "__new_primary_file_spades_collection|001_spades_graph_k063__": {"id": "a25bf1948a88d3a6", "src": "hda", "uuid": "52e70d76-3e2d-4de8-ac90-4196f1886012"}, "__new_primary_file_spades_collection|001_spades_graph_k077__": {"id": "50b73668c24e41d5", "src": "hda", "uuid": "3fd7f87a-2a01-4896-853c-23f45afff5fc"}, "__new_primary_file_spades_collection|001_spades_graph_k089__": {"id": "fd04d8a1cbe2b97a", "src": "hda", "uuid": "2d3e3648-9f22-4dca-87d6-becc9fcd6518"}, "__new_primary_file_spades_collection|001_spades_graph_k099__": {"id": "1611edde0f518852", "src": "hda", "uuid": "1b7997e7-ca4a-4f5b-a367-975ccdaa815c"}, "__new_primary_file_spades_collection|001_spades_graph_k107__": {"id": "2fe056efb5e142a4", "src": "hda", "uuid": "65151349-5656-4841-89d7-0d0c3607b485"}, "__new_primary_file_spades_collection|001_spades_graph_k115__": {"id": "1ab5da2c4f8d085f", "src": "hda", "uuid": "befda056-2594-428d-b093-407ceb4a761e"}, "__new_primary_file_spades_collection|001_spades_graph_k121__": {"id": "f31364cfb18f8a81", "src": "hda", "uuid": "080a8ef4-8464-44c1-af33-2f68ec879569"}, "__new_primary_file_spades_collection|001_spades_graph_k127__": {"id": "3ff301851f37a1df", "src": "hda", "uuid": "8a16fc4e-a8b2-4c12-b7a8-f56197464250"}, "__new_primary_file_spades_collection|002_depth_filter__": {"id": "35f84111fd7775c6", "src": "hda", "uuid": "195e0dbd-5124-4620-be15-33a2d1e7f7e9"}, "__new_primary_file_spades_collection|003_overlaps_removed__": {"id": "c7a1bf92465a7440", "src": "hda", "uuid": "015c200d-8cdc-4e20-bd29-91bff835f9ed"}, "__new_primary_file_spades_collection|004_bridges_applied__": {"id": "ecd518f8c8e78b05", "src": "hda", "uuid": "05564682-f24a-4e3e-8e8d-9bb4b90748ac"}, "__new_primary_file_spades_collection|005_final_clean__": {"id": "3fdac4cc9c09299e", "src": "hda", "uuid": "eb85f669-e750-4fd0-a640-a4d56bde5d81"}}, "output_collections": {"spades_collection": {"id": "ddd7b7f231ac291f", "src": "hdca"}}, "tool_stdout": "\nStarting Unicycler (2025-01-14 13:23:12)\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 8 -o ./ --verbosity 3 -1 fq1.fastq -2 fq2.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --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_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 1\n\nUnicycler version: v0.5.1\nUsing 8 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/133/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 4.0.0 good /usr/local/bin/spades.py \n racon not used \n makeblastdb 2.16.0+ good /usr/local/bin/makeblastdb\n tblastn 2.16.0+ good /usr/local/bin/tblastn \n\n\nChoosing k-mer range for assembly (2025-01-14 13:23:12)\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 (2025-01-14 13:23:12)\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\nspades.py -o /galaxy/server/database/jobs_directory/000/133/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/133/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/133/working/fq2.fastq -m 1024\n== Warning == output dir is not empty! Please, clean output directory before run.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/133/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/133/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/133/working/fq2.fastq -m 1024\n\nSystem information:\n SPAdes version: 4.0.0\n Python version: 3.12.4\n OS: Linux-6.1.112+-x86_64-with-glibc2.36\nOutput dir: /galaxy/server/database/jobs_directory/000/133/working/spades_assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Isolate mode\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/133/working/fq1.fastq']\n right reads: ['/galaxy/server/database/jobs_directory/000/133/working/fq2.fastq']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\n Assembly graph output will use GFA v1.1 format\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/tmp\n Threads: 8\n Memory limit (in Gb): 1024\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/spades.log\n/galaxy/server/database/jobs_directory/000/133/working/fq1.fastq: max reads length: 251\n/galaxy/server/database/jobs_directory/000/133/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/000/133/working/spades_assembly/K27/configs/config.info /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K27/configs/isolate_mode.info\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K27/configs/config.info\"\n 0:00:00.001 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K27/configs/isolate_mode.info\"\n 0:00:00.001 1M / 20M INFO General (memory_limit.cpp : 55) Memory limit set to 1024 Gb\n 0:00:00.001 1M / 20M INFO General (main.cpp : 102) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.001 1M / 20M INFO General (main.cpp : 103) Maximum k-mer length: 128\n 0:00:00.001 1M / 20M INFO General (main.cpp : 104) Assembling dataset (\"/galaxy/server/database/jobs_directory/000/133/working/spades_assembly/dataset.info\") with K=27\n 0:00:00.001 1M / 20M INFO General (main.cpp : 105) Maximum # of threads to use (adjusted due to OMP capabilities): 8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 212) SPAdes started\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 234) Two-step repeat resolution disabled\n 0:00:00.001 1M / 20M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3\n 0:00:00.001 1M / 20M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40\n 0:00:00.001 1M / 20M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 245) Will need read mapping, kmer mapper will be attached\n 0:00:00.001 1M / 20M INFO StageManager (stage.cpp : 189) STAGE == Binary Read Conversion (id: read_conversion)\n 0:00:00.007 1M / 20M INFO General (read_converter.cpp : 78) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.007 1M / 20M INFO General (read_converter.cpp : 99) Converting paired reads\n 0:00:00.074 81M / 81M INFO General (binary_converter.cpp : 143) 7925 reads written\n 0:00:00.077 50M / 50M INFO General (read_converter.cpp : 113) Converting single reads\n 0:00:00.093 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.095 50M / 50M INFO General (read_converter.cpp : 119) Converting merged reads\n 0:00:00.104 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.143 1M / 42M INFO StageManager (stage.cpp : 189) STAGE == de Bruijn graph construction (id: construction)\n 0:00:00.162 1M / 42M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.162 1M / 42M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.162 1M / 42M INFO General (stage.cpp : 121) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)\n 0:00:00.162 1M / 42M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:00.164 1M / 42M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:00.164 1M / 42M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:00.164 1M / 42M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:00.938 1M / 55M INFO General (kmer_splitters.hpp : 134) Used 31700 reads\n 0:00:00.941 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:01.179 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 35249 kmers in total.\n 0:00:01.179 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Extension index construction (id: construction:extension_index_construction)\n 0:00:01.229 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index\n 0:00:01.229 1M / 55M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:01.230 1M / 55M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:01.230 1M / 55M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:01.230 1M / 55M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:02.005 4641M / 4641M INFO General (kmer_splitters.hpp : 197) Processed 35249 kmers\n 0:00:02.005 4641M / 4641M INFO General (kmer_splitters.hpp : 202) Used 35249 kmers.\n 0:00:02.006 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:02.247 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 34510 kmers in total.\n 0:00:02.247 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.299 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 34510 kmers, 86928 bytes occupied (20.1514 bits per kmer).\n 0:00:02.299 1M / 55M INFO General (kmer_index_builder.hpp : 168) Merging final buckets.\n 0:00:02.487 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers\n 0:00:02.500 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished.\n 0:00:02.521 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Condensing graph (id: construction:graph_condensing)\n 0:00:02.524 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths\n 0:00:02.527 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2775 sequences extracted\n 0:00:02.529 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops\n 0:00:02.533 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected\n 0:00:02.534 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges...\n 0:00:02.534 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted\n 0:00:02.534 1M / 55M INFO General (debruijn_graph_constructor: 516) Total 5550 edges to create\n 0:00:02.534 2M / 55M INFO General (debruijn_graph_constructor: 519) Collecting link records\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 521) Ordering link records\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 524) Sorting done\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords...\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 542) Total 2036 vertices to create\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 545) Connecting the graph\n 0:00:02.538 2M / 55M INFO General (stage.cpp : 121) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)\n 0:00:02.538 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.572 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 35249 kmers, 87400 bytes occupied (19.836 bits per kmer).\n 0:00:02.573 2M / 55M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.635 2M / 55M INFO General (construction.cpp : 427) Filling coverage and flanking coverage from PHM\n 0:00:02.636 2M / 55M INFO General (coverage_filling.hpp : 83) Processed 5550 edges\n 0:00:02.703 1M / 55M INFO StageManager (stage.cpp : 189) STAGE == EC Threshold Finding (id: ec_threshold_finder)\n 0:00:02.703 1M / 55M INFO General (kmer_coverage_model.cpp : 182) Kmer coverage valley at: 7\n 0:00:02.703 1M / 55M INFO General (kmer_coverage_model.cpp : 202) K-mer histogram maximum: 695\n 0:00:02.703 1M / 55M INFO General (kmer_coverage_model.cpp : 238) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.703 1M / 55M INFO General (kmer_coverage_model.cpp : 260) Fitting coverage model\n 0:00:02.822 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 2\n 0:00:03.238 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 4\n 0:00:03.860 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 8\n 0:00:04.335 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 16\n 0:00:05.141 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 32\n 0:00:05.141 1M / 55M INFO General (kmer_coverage_model.cpp : 310) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:05.142 1M / 55M INFO General (kmer_coverage_model.cpp : 335) Probability of erroneous kmer at valley: 1\n 0:00:05.142 1M / 55M INFO General (kmer_coverage_model.cpp : 359) Preliminary threshold calculated as: 275\n 0:00:05.142 1M / 55M INFO General (kmer_coverage_model.cpp : 363) Threshold adjusted to: 275\n 0:00:05.142 1M / 55M INFO General (kmer_coverage_model.cpp : 376) Estimated genome size (ignoring repeats): 5132\n 0:00:05.142 1M / 55M INFO General (genomic_info_filler.cpp : 56) Mean coverage was calculated as 671.577\n 0:00:05.142 1M / 55M INFO General (genomic_info_filler.cpp : 71) EC coverage threshold value was calculated as 275\n 0:00:05.142 1M / 55M INFO General (genomic_info_filler.cpp : 72) Trusted kmer low bound: 0\n 0:00:05.142 1M / 55M INFO StageManager (stage.cpp : 189\n..\nmbly/K127/scaffolds.fasta\n 0:00:04.983 3M / 160M INFO General (contig_output_stage.cpp : 107) Outputting FastG paths to /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/scaffolds.paths\n 0:00:04.988 3M / 160M INFO General (contig_output_stage.cpp : 114) Populating GFA with scaffold paths\n 0:00:04.997 3M / 160M INFO General (pipeline.cpp : 292) SPAdes finished\n 0:00:04.999 1M / 160M INFO General (main.cpp : 131) Assembling time: 0 hours 0 minutes 5 seconds\n===== K127 finished.\n===== Copy files started.\n== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/before_rr.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/before_rr.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/final_contigs.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/contigs.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/strain_graph.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/strain_graph.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/scaffolds.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/scaffolds.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/scaffolds.paths /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/scaffolds.paths /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/final_contigs.paths /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/contigs.paths\n===== Copy files finished.\n===== Assembling finished.\n===== Breaking scaffolds started.\n== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/scaffolds.fasta --misc_dir /galaxy/server/database/jobs_directory/000/133/working/spades_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/000/133/working/spades_assembly/contigs.fasta\n * Assembled scaffolds are in /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/scaffolds.fasta\n * Paths in the assembly graph corresponding to the contigs are in /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/contigs.paths\n * Paths in the assembly graph corresponding to the scaffolds are in /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/scaffolds.paths\n * Assembly graph is in /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/assembly_graph.fastg\n * Assembly graph in GFA format is in /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/assembly_graph_with_scaffolds.gfa\n======= SPAdes pipeline finished.\nSPAdes log can be found here: /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/spades.log\nThank you for using SPAdes! If you use it in your research, please cite:\n Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. and Korobeynikov, A., 2020. Using SPAdes de novo assembler. Current protocols in bioinformatics, 70(1), p.e102.\n doi.org/10.1002/cpbi.102\n\n\nInsert size mean: 367.3 bp\nInsert size stdev: 37.3 bp\n\n\nCleaning k27 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k027_assembly_graph.gfa\n\nCleaning k47 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k047_assembly_graph.gfa\n\nCleaning k63 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k063_assembly_graph.gfa\n\nCleaning k77 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k077_assembly_graph.gfa\n\nCleaning k89 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k089_assembly_graph.gfa\n\nCleaning k99 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k099_assembly_graph.gfa\n\nCleaning k107 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k107_assembly_graph.gfa\n\nCleaning k115 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k115_assembly_graph.gfa\n\nCleaning k121 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k121_assembly_graph.gfa\n\nCleaning k127 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k27_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2025-01-14 13:25:32)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 1 1 5,413 5,413 5,413 0 5.00e-01 <-best\n 47 1 1 5,433 5,433 5,433 0 5.00e-01\n 63 1 1 5,449 5,449 5,449 0 5.00e-01\n 77 1 1 5,463 5,463 5,463 0 5.00e-01\n 89 1 1 5,475 5,475 5,475 0 5.00e-01\n 99 1 1 5,485 5,485 5,485 0 5.00e-01\n 107 1 1 5,493 5,493 5,493 0 5.00e-01\n 115 1 1 5,501 5,501 5,501 0 5.00e-01\n 121 1 1 5,507 5,507 5,507 0 5.00e-01\n 127 1 1 5,513 5,513 5,513 0 5.00e-01\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/\n\n\nDetermining graph multiplicity (2025-01-14 13:25:32)\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/000/133/working/002_depth_filter.gfa\n\n\nCleaning graph (2025-01-14 13:25:32)\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 13 14\nGraph overlaps removed\n\nSaving /galaxy/server/database/jobs_directory/000/133/working/003_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 (2025-01-14 13:25:32)\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 (2025-01-14 13:25:32)\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 (2025-01-14 13:25:32)\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/000/133/working/004_bridges_applied.gfa\n\n\nCleaning up leftover segments (2025-01-14 13:25:32)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2025-01-14 13:25:32)\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/000/133/working/005_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 (2025-01-14 13:25:32)\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/python3.12/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 (2025-01-14 13:25:41)\nSaving /galaxy/server/database/jobs_directory/000/133/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/133/working/assembly.fasta\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\nStarting Unicycler (2025-01-14 13:23:12)\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 8 -o ./ --verbosity 3 -1 fq1.fastq -2 fq2.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --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_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 1\n\nUnicycler version: v0.5.1\nUsing 8 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/133/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 4.0.0 good /usr/local/bin/spades.py \n racon not used \n makeblastdb 2.16.0+ good /usr/local/bin/makeblastdb\n tblastn 2.16.0+ good /usr/local/bin/tblastn \n\n\nChoosing k-mer range for assembly (2025-01-14 13:23:12)\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 (2025-01-14 13:23:12)\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\nspades.py -o /galaxy/server/database/jobs_directory/000/133/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/133/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/133/working/fq2.fastq -m 1024\n== Warning == output dir is not empty! Please, clean output directory before run.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/133/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/133/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/133/working/fq2.fastq -m 1024\n\nSystem information:\n SPAdes version: 4.0.0\n Python version: 3.12.4\n OS: Linux-6.1.112+-x86_64-with-glibc2.36\nOutput dir: /galaxy/server/database/jobs_directory/000/133/working/spades_assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Isolate mode\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/133/working/fq1.fastq']\n right reads: ['/galaxy/server/database/jobs_directory/000/133/working/fq2.fastq']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\n Assembly graph output will use GFA v1.1 format\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/tmp\n Threads: 8\n Memory limit (in Gb): 1024\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/spades.log\n/galaxy/server/database/jobs_directory/000/133/working/fq1.fastq: max reads length: 251\n/galaxy/server/database/jobs_directory/000/133/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/000/133/working/spades_assembly/K27/configs/config.info /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K27/configs/isolate_mode.info\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K27/configs/config.info\"\n 0:00:00.001 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K27/configs/isolate_mode.info\"\n 0:00:00.001 1M / 20M INFO General (memory_limit.cpp : 55) Memory limit set to 1024 Gb\n 0:00:00.001 1M / 20M INFO General (main.cpp : 102) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.001 1M / 20M INFO General (main.cpp : 103) Maximum k-mer length: 128\n 0:00:00.001 1M / 20M INFO General (main.cpp : 104) Assembling dataset (\"/galaxy/server/database/jobs_directory/000/133/working/spades_assembly/dataset.info\") with K=27\n 0:00:00.001 1M / 20M INFO General (main.cpp : 105) Maximum # of threads to use (adjusted due to OMP capabilities): 8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 212) SPAdes started\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 234) Two-step repeat resolution disabled\n 0:00:00.001 1M / 20M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3\n 0:00:00.001 1M / 20M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40\n 0:00:00.001 1M / 20M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 245) Will need read mapping, kmer mapper will be attached\n 0:00:00.001 1M / 20M INFO StageManager (stage.cpp : 189) STAGE == Binary Read Conversion (id: read_conversion)\n 0:00:00.007 1M / 20M INFO General (read_converter.cpp : 78) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.007 1M / 20M INFO General (read_converter.cpp : 99) Converting paired reads\n 0:00:00.074 81M / 81M INFO General (binary_converter.cpp : 143) 7925 reads written\n 0:00:00.077 50M / 50M INFO General (read_converter.cpp : 113) Converting single reads\n 0:00:00.093 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.095 50M / 50M INFO General (read_converter.cpp : 119) Converting merged reads\n 0:00:00.104 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.143 1M / 42M INFO StageManager (stage.cpp : 189) STAGE == de Bruijn graph construction (id: construction)\n 0:00:00.162 1M / 42M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.162 1M / 42M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.162 1M / 42M INFO General (stage.cpp : 121) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)\n 0:00:00.162 1M / 42M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:00.164 1M / 42M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:00.164 1M / 42M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:00.164 1M / 42M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:00.938 1M / 55M INFO General (kmer_splitters.hpp : 134) Used 31700 reads\n 0:00:00.941 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:01.179 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 35249 kmers in total.\n 0:00:01.179 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Extension index construction (id: construction:extension_index_construction)\n 0:00:01.229 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index\n 0:00:01.229 1M / 55M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:01.230 1M / 55M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:01.230 1M / 55M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:01.230 1M / 55M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:02.005 4641M / 4641M INFO General (kmer_splitters.hpp : 197) Processed 35249 kmers\n 0:00:02.005 4641M / 4641M INFO General (kmer_splitters.hpp : 202) Used 35249 kmers.\n 0:00:02.006 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:02.247 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 34510 kmers in total.\n 0:00:02.247 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.299 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 34510 kmers, 86928 bytes occupied (20.1514 bits per kmer).\n 0:00:02.299 1M / 55M INFO General (kmer_index_builder.hpp : 168) Merging final buckets.\n 0:00:02.487 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers\n 0:00:02.500 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished.\n 0:00:02.521 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Condensing graph (id: construction:graph_condensing)\n 0:00:02.524 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths\n 0:00:02.527 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2775 sequences extracted\n 0:00:02.529 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops\n 0:00:02.533 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected\n 0:00:02.534 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges...\n 0:00:02.534 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted\n 0:00:02.534 1M / 55M INFO General (debruijn_graph_constructor: 516) Total 5550 edges to create\n 0:00:02.534 2M / 55M INFO General (debruijn_graph_constructor: 519) Collecting link records\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 521) Ordering link records\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 524) Sorting done\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords...\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 542) Total 2036 vertices to create\n 0:00:02.536 2M / 55M INFO General (debruijn_graph_constructor: 545) Connecting the graph\n 0:00:02.538 2M / 55M INFO General (stage.cpp : 121) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)\n 0:00:02.538 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.572 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 35249 kmers, 87400 bytes occupied (19.836 bits per kmer).\n 0:00:02.573 2M / 55M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.635 2M / 55M INFO General (construction.cpp : 427) Filling coverage and flanking coverage from PHM\n 0:00:02.636 2M / 55M INFO General (coverage_filling.hpp : 83) Processed 5550 edges\n 0:00:02.703 1M / 55M INFO StageManager (stage.cpp : 189) STAGE == EC Threshold Finding (id: ec_threshold_finder)\n 0:00:02.703 1M / 55M INFO General (kmer_coverage_model.cpp : 182) Kmer coverage valley at: 7\n 0:00:02.703 1M / 55M INFO General (kmer_coverage_model.cpp : 202) K-mer histogram maximum: 695\n 0:00:02.703 1M / 55M INFO General (kmer_coverage_model.cpp : 238) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.703 1M / 55M INFO General (kmer_coverage_model.cpp : 260) Fitting coverage model\n 0:00:02.822 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 2\n 0:00:03.238 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 4\n 0:00:03.860 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 8\n 0:00:04.335 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 16\n 0:00:05.141 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 32\n 0:00:05.141 1M / 55M INFO General (kmer_coverage_model.cpp : 310) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:05.142 1M / 55M INFO General (kmer_coverage_model.cpp : 335) Probability of erroneous kmer at valley: 1\n 0:00:05.142 1M / 55M INFO General (kmer_coverage_model.cpp : 359) Preliminary threshold calculated as: 275\n 0:00:05.142 1M / 55M INFO General (kmer_coverage_model.cpp : 363) Threshold adjusted to: 275\n 0:00:05.142 1M / 55M INFO General (kmer_coverage_model.cpp : 376) Estimated genome size (ignoring repeats): 5132\n 0:00:05.142 1M / 55M INFO General (genomic_info_filler.cpp : 56) Mean coverage was calculated as 671.577\n 0:00:05.142 1M / 55M INFO General (genomic_info_filler.cpp : 71) EC coverage threshold value was calculated as 275\n 0:00:05.142 1M / 55M INFO General (genomic_info_filler.cpp : 72) Trusted kmer low bound: 0\n 0:00:05.142 1M / 55M INFO StageManager (stage.cpp : 189\n..\nmbly/K127/scaffolds.fasta\n 0:00:04.983 3M / 160M INFO General (contig_output_stage.cpp : 107) Outputting FastG paths to /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/scaffolds.paths\n 0:00:04.988 3M / 160M INFO General (contig_output_stage.cpp : 114) Populating GFA with scaffold paths\n 0:00:04.997 3M / 160M INFO General (pipeline.cpp : 292) SPAdes finished\n 0:00:04.999 1M / 160M INFO General (main.cpp : 131) Assembling time: 0 hours 0 minutes 5 seconds\n===== K127 finished.\n===== Copy files started.\n== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/before_rr.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/before_rr.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/assembly_graph_after_simplification.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/final_contigs.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/contigs.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/first_pe_contigs.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/strain_graph.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/strain_graph.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/scaffolds.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/scaffolds.fasta /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/scaffolds.paths /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/scaffolds.paths /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/assembly_graph_with_scaffolds.gfa /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/assembly_graph.fastg /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/K127/final_contigs.paths /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/contigs.paths\n===== Copy files finished.\n===== Assembling finished.\n===== Breaking scaffolds started.\n== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/scaffolds.fasta --misc_dir /galaxy/server/database/jobs_directory/000/133/working/spades_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/000/133/working/spades_assembly/contigs.fasta\n * Assembled scaffolds are in /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/scaffolds.fasta\n * Paths in the assembly graph corresponding to the contigs are in /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/contigs.paths\n * Paths in the assembly graph corresponding to the scaffolds are in /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/scaffolds.paths\n * Assembly graph is in /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/assembly_graph.fastg\n * Assembly graph in GFA format is in /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/assembly_graph_with_scaffolds.gfa\n======= SPAdes pipeline finished.\nSPAdes log can be found here: /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/spades.log\nThank you for using SPAdes! If you use it in your research, please cite:\n Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. and Korobeynikov, A., 2020. Using SPAdes de novo assembler. Current protocols in bioinformatics, 70(1), p.e102.\n doi.org/10.1002/cpbi.102\n\n\nInsert size mean: 367.3 bp\nInsert size stdev: 37.3 bp\n\n\nCleaning k27 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k027_assembly_graph.gfa\n\nCleaning k47 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k047_assembly_graph.gfa\n\nCleaning k63 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k063_assembly_graph.gfa\n\nCleaning k77 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k077_assembly_graph.gfa\n\nCleaning k89 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k089_assembly_graph.gfa\n\nCleaning k99 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k099_assembly_graph.gfa\n\nCleaning k107 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k107_assembly_graph.gfa\n\nCleaning k115 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k115_assembly_graph.gfa\n\nCleaning k121 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k121_assembly_graph.gfa\n\nCleaning k127 graph\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2025-01-14 13:25:32)\nFilter by read depth (2025-01-14 13:25:32)\nFilter homopolymer loops (2025-01-14 13:25:32)\nMerge all possible (2025-01-14 13:25:32)\nNormalise read depths (2025-01-14 13:25:32)\nRemove zero length segments (2025-01-14 13:25:32)\nSort link order (2025-01-14 13:25:32)\nGraph cleaning finished (2025-01-14 13:25:32)\nSaving /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/k27_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2025-01-14 13:25:32)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 1 1 5,413 5,413 5,413 0 5.00e-01 <-best\n 47 1 1 5,433 5,433 5,433 0 5.00e-01\n 63 1 1 5,449 5,449 5,449 0 5.00e-01\n 77 1 1 5,463 5,463 5,463 0 5.00e-01\n 89 1 1 5,475 5,475 5,475 0 5.00e-01\n 99 1 1 5,485 5,485 5,485 0 5.00e-01\n 107 1 1 5,493 5,493 5,493 0 5.00e-01\n 115 1 1 5,501 5,501 5,501 0 5.00e-01\n 121 1 1 5,507 5,507 5,507 0 5.00e-01\n 127 1 1 5,513 5,513 5,513 0 5.00e-01\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/133/working/spades_assembly/\n\n\nDetermining graph multiplicity (2025-01-14 13:25:32)\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/000/133/working/002_depth_filter.gfa\n\n\nCleaning graph (2025-01-14 13:25:32)\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 13 14\nGraph overlaps removed\n\nSaving /galaxy/server/database/jobs_directory/000/133/working/003_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 (2025-01-14 13:25:32)\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 (2025-01-14 13:25:32)\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 (2025-01-14 13:25:32)\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/000/133/working/004_bridges_applied.gfa\n\n\nCleaning up leftover segments (2025-01-14 13:25:32)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2025-01-14 13:25:32)\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/000/133/working/005_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 (2025-01-14 13:25:32)\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/python3.12/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 (2025-01-14 13:25:41)\nSaving /galaxy/server/database/jobs_directory/000/133/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/133/working/assembly.fasta\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 minutes", "plugin": "core", "name": "runtime_seconds", "raw_value": "149.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:25:41", "plugin": "core", "name": "end_epoch", "raw_value": "1736861141.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:23:12", "plugin": "core", "name": "start_epoch", "raw_value": "1736860992.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "unicycler/0.5.1+galaxy0-6", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.5.1+galaxy0", "test_index": 6, "time_seconds": 175.45996475219727, "inputs": {"paired_unpaired|fastq_input1": {"src": "hda", "id": "5b3e62e1ffa8c393"}, "paired_unpaired|fastq_input2": {"src": "hda", "id": "bfcea19bfdadace0"}, "paired_unpaired|fastq_input_selector": "paired", "long": {"src": "hda", "id": "5aceb46017159497"}, "mode": "normal", "keep": "2"}, "job": {"model_class": "Job", "id": "e693ca82ce43d2f8", "state": "error", "exit_code": null, "update_time": "2025-01-14T13:28:48.505416", "create_time": "2025-01-14T13:26:15.700977", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-hkmrb", "command_line": "ln -s '/galaxy/server/database/objects/a/8/e/dataset_a8e7667e-3e06-4941-833a-173c42cb310d.dat' fq1.fastq && ln -s '/galaxy/server/database/objects/7/3/8/dataset_738fb138-e581-4661-98b6-3d90bc357e56.dat' fq2.fastq && ln -s '/galaxy/server/database/objects/6/6/4/dataset_664606f8-030b-409a-8205-6ded7a8045fd.dat' 'lr.fasta' && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 -1 'fq1.fastq' -2 'fq2.fastq' -l lr.fasta --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --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_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2' --keep 2 && mkdir 'spades_graphs' && mv 00*gfa './spades_graphs/' && samtools view -@ \"${GALAXY_SLOTS:-4}\" -u 'read_alignment/long_read_alignments.sam' | samtools sort -@ \"${GALAXY_SLOTS:-4}\" -o 'read_alignment/long_read_alignments.bam'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "reuse": "[]", "keep": "\"2\"", "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"no_simple_bridges\": false, \"scores\": \"3,-6,-5,-2\"}", "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", "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\"}", "min_anchor_seg_len": "\"\"", "linear_seqs": "\"0\"", "min_fasta_length": "\"100\"", "mode": "\"normal\"", "paired_unpaired": "{\"__current_case__\": 0, \"fastq_input1\": {\"values\": [{\"id\": 175, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 176, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"paired\"}"}, "inputs": {"paired_unpaired|fastq_input1": {"id": "5b3e62e1ffa8c393", "src": "hda", "uuid": "a8e7667e-3e06-4941-833a-173c42cb310d"}, "paired_unpaired|fastq_input2": {"id": "bfcea19bfdadace0", "src": "hda", "uuid": "738fb138-e581-4661-98b6-3d90bc357e56"}, "long": {"id": "5aceb46017159497", "src": "hda", "uuid": "664606f8-030b-409a-8205-6ded7a8045fd"}}, "outputs": {"assembly_graph": {"id": "baaeb697833af929", "src": "hda", "uuid": "47cff645-4a58-4097-85ed-8615d0c178f3"}, "assembly": {"id": "ea258d7a926adca1", "src": "hda", "uuid": "ab428f4c-4d1c-4507-b764-a1f500f5ccde"}, "bam_file": {"id": "83cc9c9255d88d7e", "src": "hda", "uuid": "2f09dae1-4821-4429-84c6-df5b3b7d03ab"}}, "output_collections": {"spades_collection": {"id": "7dc5a28cdd92d68e", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stderr": "", "stdout": "", "job_messages": null, "dependencies": [], "user_email": "tests@fake.org", "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, exit_code: None, stderr: .", "Output collection 'spades_collection': expected to have 14 elements, but it had 0."], "status": "failure"}}, {"id": "unicycler/0.5.1+galaxy0-7", "has_data": true, "data": {"tool_id": "unicycler", "tool_version": "0.5.1+galaxy0", "test_index": 7, "time_seconds": 182.2201051712036, "inputs": {"paired_unpaired|fastq_input1": {"src": "hda", "id": "2bdbc033fc7ee509"}, "paired_unpaired|fastq_input2": {"src": "hda", "id": "809c769c23542a1b"}, "paired_unpaired|fastq_input_selector": "paired", "long": {"src": "hda", "id": "9f11487ed49785c9"}, "mode": "normal", "lr_align|no_simple_bridges": true, "keep": "0"}, "job": {"model_class": "Job", "id": "e7a83eb3d4b88a6e", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T13:31:50.584192", "create_time": "2025-01-14T13:29:11.254412", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-tjh6g", "command_line": "ln -s '/galaxy/server/database/objects/f/c/e/dataset_fce0fec6-34f3-495c-8fd7-d436e95cf14b.dat' fq1.fastq && ln -s '/galaxy/server/database/objects/1/7/6/dataset_176c4e5f-f5da-468e-87ba-c8c3e5ab0604.dat' fq2.fastq && ln -s '/galaxy/server/database/objects/0/e/f/dataset_0efed3d4-8a2c-402d-866b-72dffa34f24e.dat' 'lr.fasta' && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 -1 'fq1.fastq' -2 'fq2.fastq' -l lr.fasta --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --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_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2' --no_simple_bridges --keep 0", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "reuse": "[]", "keep": "\"0\"", "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"no_simple_bridges\": true, \"scores\": \"3,-6,-5,-2\"}", "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", "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\"}", "min_anchor_seg_len": "\"\"", "linear_seqs": "\"0\"", "min_fasta_length": "\"100\"", "mode": "\"normal\"", "paired_unpaired": "{\"__current_case__\": 0, \"fastq_input1\": {\"values\": [{\"id\": 181, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 182, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"paired\"}"}, "inputs": {"paired_unpaired|fastq_input1": {"id": "2bdbc033fc7ee509", "src": "hda", "uuid": "fce0fec6-34f3-495c-8fd7-d436e95cf14b"}, "paired_unpaired|fastq_input2": {"id": "809c769c23542a1b", "src": "hda", "uuid": "176c4e5f-f5da-468e-87ba-c8c3e5ab0604"}, "long": {"id": "9f11487ed49785c9", "src": "hda", "uuid": "0efed3d4-8a2c-402d-866b-72dffa34f24e"}}, "outputs": {"assembly_graph": {"id": "decf1a3734b6a69a", "src": "hda", "uuid": "0809585f-c0df-470e-88ca-42c2c8a33763"}, "assembly": {"id": "f2468ad3ead6b276", "src": "hda", "uuid": "3542357f-cd66-4fa5-87fe-77a4b48faefd"}}, "output_collections": {}, "tool_stdout": "\nStarting Unicycler (2025-01-14 13:29:13)\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 8 -o ./ --verbosity 3 -1 fq1.fastq -2 fq2.fastq -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --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_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --no_simple_bridges --keep 0\n\nUnicycler version: v0.5.1\nUsing 8 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/141/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 4.0.0 good /usr/local/bin/spades.py \n racon 1.5.0 good /usr/local/bin/racon \n makeblastdb 2.16.0+ good /usr/local/bin/makeblastdb\n tblastn 2.16.0+ good /usr/local/bin/tblastn \n\n\nChoosing k-mer range for assembly (2025-01-14 13:29:13)\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 (2025-01-14 13:29:13)\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\nspades.py -o /galaxy/server/database/jobs_directory/000/141/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/141/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/141/working/fq2.fastq -m 1024\n== Warning == output dir is not empty! Please, clean output directory before run.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/141/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/141/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/141/working/fq2.fastq -m 1024\n\nSystem information:\n SPAdes version: 4.0.0\n Python version: 3.12.4\n OS: Linux-6.1.112+-x86_64-with-glibc2.36\nOutput dir: /galaxy/server/database/jobs_directory/000/141/working/spades_assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Isolate mode\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/141/working/fq1.fastq']\n right reads: ['/galaxy/server/database/jobs_directory/000/141/working/fq2.fastq']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\n Assembly graph output will use GFA v1.1 format\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/tmp\n Threads: 8\n Memory limit (in Gb): 1024\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/spades.log\n/galaxy/server/database/jobs_directory/000/141/working/fq1.fastq: max reads length: 251\n/galaxy/server/database/jobs_directory/000/141/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/000/141/working/spades_assembly/K27/configs/config.info /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/K27/configs/isolate_mode.info\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/141/working/spades_assembly/K27/configs/config.info\"\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/141/working/spades_assembly/K27/configs/isolate_mode.info\"\n 0:00:00.000 1M / 20M INFO General (memory_limit.cpp : 55) Memory limit set to 1024 Gb\n 0:00:00.000 1M / 20M INFO General (main.cpp : 102) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 1M / 20M INFO General (main.cpp : 103) Maximum k-mer length: 128\n 0:00:00.000 1M / 20M INFO General (main.cpp : 104) Assembling dataset (\"/galaxy/server/database/jobs_directory/000/141/working/spades_assembly/dataset.info\") with K=27\n 0:00:00.000 1M / 20M INFO General (main.cpp : 105) Maximum # of threads to use (adjusted due to OMP capabilities): 8\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 212) SPAdes started\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 234) Two-step repeat resolution disabled\n 0:00:00.000 1M / 20M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3\n 0:00:00.000 1M / 20M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40\n 0:00:00.001 1M / 20M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 245) Will need read mapping, kmer mapper will be attached\n 0:00:00.001 1M / 20M INFO StageManager (stage.cpp : 189) STAGE == Binary Read Conversion (id: read_conversion)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 78) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 99) Converting paired reads\n 0:00:00.070 81M / 81M INFO General (binary_converter.cpp : 143) 7925 reads written\n 0:00:00.074 50M / 50M INFO General (read_converter.cpp : 113) Converting single reads\n 0:00:00.088 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.090 50M / 50M INFO General (read_converter.cpp : 119) Converting merged reads\n 0:00:00.097 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.131 1M / 42M INFO StageManager (stage.cpp : 189) STAGE == de Bruijn graph construction (id: construction)\n 0:00:00.148 1M / 42M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.148 1M / 42M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.148 1M / 42M INFO General (stage.cpp : 121) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)\n 0:00:00.148 1M / 42M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:00.149 1M / 42M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:00.150 1M / 42M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:00.150 1M / 42M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:00.906 1M / 55M INFO General (kmer_splitters.hpp : 134) Used 31700 reads\n 0:00:00.909 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:01.129 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 35249 kmers in total.\n 0:00:01.129 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Extension index construction (id: construction:extension_index_construction)\n 0:00:01.170 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index\n 0:00:01.170 1M / 55M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:01.171 1M / 55M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:01.171 1M / 55M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:01.171 1M / 55M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:01.986 4641M / 4641M INFO General (kmer_splitters.hpp : 197) Processed 35249 kmers\n 0:00:01.986 4641M / 4641M INFO General (kmer_splitters.hpp : 202) Used 35249 kmers.\n 0:00:01.987 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:02.227 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 34510 kmers in total.\n 0:00:02.227 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.284 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 34510 kmers, 86928 bytes occupied (20.1514 bits per kmer).\n 0:00:02.284 1M / 55M INFO General (kmer_index_builder.hpp : 168) Merging final buckets.\n 0:00:02.480 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers\n 0:00:02.494 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished.\n 0:00:02.518 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Condensing graph (id: construction:graph_condensing)\n 0:00:02.521 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths\n 0:00:02.525 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2775 sequences extracted\n 0:00:02.527 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops\n 0:00:02.531 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected\n 0:00:02.531 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges...\n 0:00:02.532 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted\n 0:00:02.532 1M / 55M INFO General (debruijn_graph_constructor: 516) Total 5550 edges to create\n 0:00:02.532 2M / 55M INFO General (debruijn_graph_constructor: 519) Collecting link records\n 0:00:02.533 2M / 55M INFO General (debruijn_graph_constructor: 521) Ordering link records\n 0:00:02.533 2M / 55M INFO General (debruijn_graph_constructor: 524) Sorting done\n 0:00:02.533 2M / 55M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords...\n 0:00:02.534 2M / 55M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted\n 0:00:02.534 2M / 55M INFO General (debruijn_graph_constructor: 542) Total 2036 vertices to create\n 0:00:02.534 2M / 55M INFO General (debruijn_graph_constructor: 545) Connecting the graph\n 0:00:02.536 2M / 55M INFO General (stage.cpp : 121) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)\n 0:00:02.536 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.570 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 35249 kmers, 87400 bytes occupied (19.836 bits per kmer).\n 0:00:02.571 2M / 55M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.641 2M / 55M INFO General (construction.cpp : 427) Filling coverage and flanking coverage from PHM\n 0:00:02.643 2M / 55M INFO General (coverage_filling.hpp : 83) Processed 5550 edges\n 0:00:02.709 1M / 55M INFO StageManager (stage.cpp : 189) STAGE == EC Threshold Finding (id: ec_threshold_finder)\n 0:00:02.709 1M / 55M INFO General (kmer_coverage_model.cpp : 182) Kmer coverage valley at: 7\n 0:00:02.709 1M / 55M INFO General (kmer_coverage_model.cpp : 202) K-mer histogram maximum: 695\n 0:00:02.709 1M / 55M INFO General (kmer_coverage_model.cpp : 238) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.709 1M / 55M INFO General (kmer_coverage_model.cpp : 260) Fitting coverage model\n 0:00:02.830 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 2\n 0:00:03.251 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 4\n 0:00:03.875 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 8\n 0:00:04.356 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 16\n 0:00:05.177 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 32\n 0:00:05.177 1M / 55M INFO General (kmer_coverage_model.cpp : 310) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:05.179 1M / 55M INFO General (kmer_coverage_model.cpp : 335) Probability of erroneous kmer at valley: 1\n 0:00:05.179 1M / 55M INFO General (kmer_coverage_model.cpp : 359) Preliminary threshold calculated as: 275\n 0:00:05.179 1M / 55M INFO General (kmer_coverage_model.cpp : 363) Threshold adjusted to: 275\n 0:00:05.179 1M / 55M INFO General (kmer_coverage_model.cpp : 376) Estimated genome size (ignoring repeats): 5132\n 0:00:05.179 1M / 55M INFO General (genomic_info_filler.cpp : 56) Mean coverage was calculated as 671.577\n 0:00:05.179 1M / 55M INFO General (genomic_info_filler.cpp : 71) EC coverage threshold value was calculated as 275\n 0:00:05.179 1M / 55M INFO General (genomic_info_filler.cpp : 72) Trusted kmer low bound: 0\n 0:00:05.179 1M / 55M INFO StageManager (stage.cpp \n..\nength segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k027_assembly_graph.gfa\n\nCleaning k47 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k047_assembly_graph.gfa\n\nCleaning k63 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k063_assembly_graph.gfa\n\nCleaning k77 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k077_assembly_graph.gfa\n\nCleaning k89 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k089_assembly_graph.gfa\n\nCleaning k99 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k099_assembly_graph.gfa\n\nCleaning k107 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k107_assembly_graph.gfa\n\nCleaning k115 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k115_assembly_graph.gfa\n\nCleaning k121 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k121_assembly_graph.gfa\n\nCleaning k127 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k27_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2025-01-14 13:31:32)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 1 1 5,413 5,413 5,413 0 5.00e-01 <-best\n 47 1 1 5,433 5,433 5,433 0 5.00e-01\n 63 1 1 5,449 5,449 5,449 0 5.00e-01\n 77 1 1 5,463 5,463 5,463 0 5.00e-01\n 89 1 1 5,475 5,475 5,475 0 5.00e-01\n 99 1 1 5,485 5,485 5,485 0 5.00e-01\n 107 1 1 5,493 5,493 5,493 0 5.00e-01\n 115 1 1 5,501 5,501 5,501 0 5.00e-01\n 121 1 1 5,507 5,507 5,507 0 5.00e-01\n 127 1 1 5,513 5,513 5,513 0 5.00e-01\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k027.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k047.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k063.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k077.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k089.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k099.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k107.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k115.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k121.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k127.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/\n\n\nDetermining graph multiplicity (2025-01-14 13:31:32)\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\n\nCleaning graph (2025-01-14 13:31:32)\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 13 14\nGraph overlaps removed\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 (2025-01-14 13:31:32)\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 (2025-01-14 13:31:32)\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 (2025-01-14 13:31:32)\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 (2025-01-14 13:31:32)\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/000/141/working/miniasm_assembly/all_segments.fasta\n1\t5386\t3\t5158\t+\t1\t5386\t227\t5382\t5155\t5155\t255\tcm:i:1149\n1\t5386\t5163\t5383\t+\t1\t5386\t1\t221\t220\t220\t255\tcm:i:47\nNumber of minimap alignments: 1\n\nSaving to /galaxy/server/database/jobs_directory/000/141/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\nDetermining low score threshold (2025-01-14 13:31:32)\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 (2025-01-14 13:31:32)\n1\t5386\t5\t5161\t+\t1\t5386\t229\t5385\t5156\t5156\t255\tcm:i:959\n1\t5386\t5168\t5384\t+\t1\t5386\t6\t222\t216\t216\t255\tcm:i:39\n\nDone! 1 out of 1 reads aligned\n\n\nAligning reads (2025-01-14 13:31:32)\n1/1: 1 (5386 bp)\nminimap alignments:\n 5,5161,+,1,229,5385\n 5168,5384,+,1,6,222\nReference ranges:\n 1+: 0 - 5386\nRange: 1: 0 - 5386\n common 10-mers: 5464\n line 1: 215 points, score=213.009259 (good)\n line 2: 5153 points, score=5151.000388 (good)\nAll Seqan alignments (time to align = 0.058 s):\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 0 224 5162 5386 + 672 100.00 100.00%\n 1 224 5386 0 5162 + 15486 100.00 100.00%\nFinal alignments:\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 224 5386 0 5162 + 15486 100.00 100.00%\n 1 0 224 5162 5386 + 672 100.00 100.00%\n\n\nRead alignment summary (2025-01-14 13:31:32)\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/000/141/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 (2025-01-14 13:31:32)\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 (2025-01-14 13:31:32)\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\n\nCleaning up leftover segments (2025-01-14 13:31:32)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2025-01-14 13:31:32)\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\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 (2025-01-14 13:31:32)\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/python3.12/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 (2025-01-14 13:31:41)\nSaving /galaxy/server/database/jobs_directory/000/141/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/141/working/assembly.fasta\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "\nStarting Unicycler (2025-01-14 13:29:13)\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 8 -o ./ --verbosity 3 -1 fq1.fastq -2 fq2.fastq -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --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_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --no_simple_bridges --keep 0\n\nUnicycler version: v0.5.1\nUsing 8 threads\n\nThe output directory already exists and files may be reused or overwritten:\n /galaxy/server/database/jobs_directory/000/141/working\n\nBridging mode: normal\n using default normal bridge quality cutoff: 10.00\n\nDependencies:\n Program Version Status Path \n spades.py 4.0.0 good /usr/local/bin/spades.py \n racon 1.5.0 good /usr/local/bin/racon \n makeblastdb 2.16.0+ good /usr/local/bin/makeblastdb\n tblastn 2.16.0+ good /usr/local/bin/tblastn \n\n\nChoosing k-mer range for assembly (2025-01-14 13:29:13)\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 (2025-01-14 13:29:13)\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\nspades.py -o /galaxy/server/database/jobs_directory/000/141/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/141/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/141/working/fq2.fastq -m 1024\n== Warning == output dir is not empty! Please, clean output directory before run.\nCommand: /usr/local/bin/spades.py -o /galaxy/server/database/jobs_directory/000/141/working/spades_assembly -k 27 --threads 8 --gfa11 --isolate -1 /galaxy/server/database/jobs_directory/000/141/working/fq1.fastq -2 /galaxy/server/database/jobs_directory/000/141/working/fq2.fastq -m 1024\n\nSystem information:\n SPAdes version: 4.0.0\n Python version: 3.12.4\n OS: Linux-6.1.112+-x86_64-with-glibc2.36\nOutput dir: /galaxy/server/database/jobs_directory/000/141/working/spades_assembly\nMode: ONLY assembling (without read error correction)\nDebug mode is turned OFF\nDataset parameters:\n Isolate mode\n Reads:\n Library number: 1, library type: paired-end\n orientation: fr\n left reads: ['/galaxy/server/database/jobs_directory/000/141/working/fq1.fastq']\n right reads: ['/galaxy/server/database/jobs_directory/000/141/working/fq2.fastq']\n interlaced reads: not specified\n single reads: not specified\n merged reads: not specified\nAssembly parameters:\n k: [27]\n Repeat resolution is enabled\n Mismatch careful mode is turned OFF\n MismatchCorrector will be SKIPPED\n Coverage cutoff is turned OFF\n Assembly graph output will use GFA v1.1 format\nOther parameters:\n Dir for temp files: /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/tmp\n Threads: 8\n Memory limit (in Gb): 1024\n======= SPAdes pipeline started. Log can be found here: /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/spades.log\n/galaxy/server/database/jobs_directory/000/141/working/fq1.fastq: max reads length: 251\n/galaxy/server/database/jobs_directory/000/141/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/000/141/working/spades_assembly/K27/configs/config.info /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/K27/configs/isolate_mode.info\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/141/working/spades_assembly/K27/configs/config.info\"\n 0:00:00.000 1M / 20M INFO General (main.cpp : 94) Loaded config from \"/galaxy/server/database/jobs_directory/000/141/working/spades_assembly/K27/configs/isolate_mode.info\"\n 0:00:00.000 1M / 20M INFO General (memory_limit.cpp : 55) Memory limit set to 1024 Gb\n 0:00:00.000 1M / 20M INFO General (main.cpp : 102) Starting SPAdes, built from N/A, git revision N/A\n 0:00:00.000 1M / 20M INFO General (main.cpp : 103) Maximum k-mer length: 128\n 0:00:00.000 1M / 20M INFO General (main.cpp : 104) Assembling dataset (\"/galaxy/server/database/jobs_directory/000/141/working/spades_assembly/dataset.info\") with K=27\n 0:00:00.000 1M / 20M INFO General (main.cpp : 105) Maximum # of threads to use (adjusted due to OMP capabilities): 8\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 212) SPAdes started\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion\n 0:00:00.000 1M / 20M INFO General (pipeline.cpp : 234) Two-step repeat resolution disabled\n 0:00:00.000 1M / 20M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3\n 0:00:00.000 1M / 20M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40\n 0:00:00.001 1M / 20M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8\n 0:00:00.001 1M / 20M INFO General (pipeline.cpp : 245) Will need read mapping, kmer mapper will be attached\n 0:00:00.001 1M / 20M INFO StageManager (stage.cpp : 189) STAGE == Binary Read Conversion (id: read_conversion)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 78) Converting reads to binary format for library #0 (takes a while)\n 0:00:00.006 1M / 20M INFO General (read_converter.cpp : 99) Converting paired reads\n 0:00:00.070 81M / 81M INFO General (binary_converter.cpp : 143) 7925 reads written\n 0:00:00.074 50M / 50M INFO General (read_converter.cpp : 113) Converting single reads\n 0:00:00.088 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.090 50M / 50M INFO General (read_converter.cpp : 119) Converting merged reads\n 0:00:00.097 63M / 63M INFO General (binary_converter.cpp : 143) 0 reads written\n 0:00:00.131 1M / 42M INFO StageManager (stage.cpp : 189) STAGE == de Bruijn graph construction (id: construction)\n 0:00:00.148 1M / 42M INFO General (construction.cpp : 150) Max read length 251\n 0:00:00.148 1M / 42M INFO General (construction.cpp : 156) Average read length 250.525\n 0:00:00.148 1M / 42M INFO General (stage.cpp : 121) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)\n 0:00:00.148 1M / 42M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:00.149 1M / 42M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:00.150 1M / 42M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:00.150 1M / 42M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:00.906 1M / 55M INFO General (kmer_splitters.hpp : 134) Used 31700 reads\n 0:00:00.909 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:01.129 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 35249 kmers in total.\n 0:00:01.129 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Extension index construction (id: construction:extension_index_construction)\n 0:00:01.170 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index\n 0:00:01.170 1M / 55M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 80 files using 8 threads. This might take a while.\n 0:00:01.171 1M / 55M INFO General (file_limit.hpp : 43) Open file limit set to 1048576\n 0:00:01.171 1M / 55M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 42.6666 Gb\n 0:00:01.171 1M / 55M INFO General (kmer_splitter.hpp : 102) Using cell size of 838860\n 0:00:01.986 4641M / 4641M INFO General (kmer_splitters.hpp : 197) Processed 35249 kmers\n 0:00:01.986 4641M / 4641M INFO General (kmer_splitters.hpp : 202) Used 35249 kmers.\n 0:00:01.987 1M / 55M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.\n 0:00:02.227 1M / 55M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 34510 kmers in total.\n 0:00:02.227 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.284 1M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 34510 kmers, 86928 bytes occupied (20.1514 bits per kmer).\n 0:00:02.284 1M / 55M INFO General (kmer_index_builder.hpp : 168) Merging final buckets.\n 0:00:02.480 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers\n 0:00:02.494 1M / 55M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished.\n 0:00:02.518 1M / 55M INFO General (stage.cpp : 121) PROCEDURE == Condensing graph (id: construction:graph_condensing)\n 0:00:02.521 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths\n 0:00:02.525 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2775 sequences extracted\n 0:00:02.527 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops\n 0:00:02.531 1M / 55M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected\n 0:00:02.531 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges...\n 0:00:02.532 1M / 55M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted\n 0:00:02.532 1M / 55M INFO General (debruijn_graph_constructor: 516) Total 5550 edges to create\n 0:00:02.532 2M / 55M INFO General (debruijn_graph_constructor: 519) Collecting link records\n 0:00:02.533 2M / 55M INFO General (debruijn_graph_constructor: 521) Ordering link records\n 0:00:02.533 2M / 55M INFO General (debruijn_graph_constructor: 524) Sorting done\n 0:00:02.533 2M / 55M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords...\n 0:00:02.534 2M / 55M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted\n 0:00:02.534 2M / 55M INFO General (debruijn_graph_constructor: 542) Total 2036 vertices to create\n 0:00:02.534 2M / 55M INFO General (debruijn_graph_constructor: 545) Connecting the graph\n 0:00:02.536 2M / 55M INFO General (stage.cpp : 121) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)\n 0:00:02.536 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices\n 0:00:02.570 2M / 55M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 35249 kmers, 87400 bytes occupied (19.836 bits per kmer).\n 0:00:02.571 2M / 55M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while.\n 0:00:02.641 2M / 55M INFO General (construction.cpp : 427) Filling coverage and flanking coverage from PHM\n 0:00:02.643 2M / 55M INFO General (coverage_filling.hpp : 83) Processed 5550 edges\n 0:00:02.709 1M / 55M INFO StageManager (stage.cpp : 189) STAGE == EC Threshold Finding (id: ec_threshold_finder)\n 0:00:02.709 1M / 55M INFO General (kmer_coverage_model.cpp : 182) Kmer coverage valley at: 7\n 0:00:02.709 1M / 55M INFO General (kmer_coverage_model.cpp : 202) K-mer histogram maximum: 695\n 0:00:02.709 1M / 55M INFO General (kmer_coverage_model.cpp : 238) Estimated median coverage: 695. Coverage mad: 91.9212\n 0:00:02.709 1M / 55M INFO General (kmer_coverage_model.cpp : 260) Fitting coverage model\n 0:00:02.830 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 2\n 0:00:03.251 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 4\n 0:00:03.875 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 8\n 0:00:04.356 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 16\n 0:00:05.177 1M / 55M INFO General (kmer_coverage_model.cpp : 296) ... iteration 32\n 0:00:05.177 1M / 55M INFO General (kmer_coverage_model.cpp : 310) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418\n 0:00:05.179 1M / 55M INFO General (kmer_coverage_model.cpp : 335) Probability of erroneous kmer at valley: 1\n 0:00:05.179 1M / 55M INFO General (kmer_coverage_model.cpp : 359) Preliminary threshold calculated as: 275\n 0:00:05.179 1M / 55M INFO General (kmer_coverage_model.cpp : 363) Threshold adjusted to: 275\n 0:00:05.179 1M / 55M INFO General (kmer_coverage_model.cpp : 376) Estimated genome size (ignoring repeats): 5132\n 0:00:05.179 1M / 55M INFO General (genomic_info_filler.cpp : 56) Mean coverage was calculated as 671.577\n 0:00:05.179 1M / 55M INFO General (genomic_info_filler.cpp : 71) EC coverage threshold value was calculated as 275\n 0:00:05.179 1M / 55M INFO General (genomic_info_filler.cpp : 72) Trusted kmer low bound: 0\n 0:00:05.179 1M / 55M INFO StageManager (stage.cpp \n..\nength segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k027_assembly_graph.gfa\n\nCleaning k47 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k047_assembly_graph.gfa\n\nCleaning k63 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k063_assembly_graph.gfa\n\nCleaning k77 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k077_assembly_graph.gfa\n\nCleaning k89 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k089_assembly_graph.gfa\n\nCleaning k99 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k099_assembly_graph.gfa\n\nCleaning k107 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k107_assembly_graph.gfa\n\nCleaning k115 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k115_assembly_graph.gfa\n\nCleaning k121 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k121_assembly_graph.gfa\n\nCleaning k127 graph\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k127_assembly_graph.gfa\n\nRepair multi way junctions (2025-01-14 13:31:32)\nFilter by read depth (2025-01-14 13:31:32)\nFilter homopolymer loops (2025-01-14 13:31:32)\nMerge all possible (2025-01-14 13:31:32)\nNormalise read depths (2025-01-14 13:31:32)\nRemove zero length segments (2025-01-14 13:31:32)\nSort link order (2025-01-14 13:31:32)\nGraph cleaning finished (2025-01-14 13:31:32)\nSaving /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/k27_assembly_graph.gfa\n\n\nSPAdes assembly graph summary (2025-01-14 13:31:32)\nK-mer Contigs Links Total length N50 Longest contig Dead ends Score \n 27 1 1 5,413 5,413 5,413 0 5.00e-01 <-best\n 47 1 1 5,433 5,433 5,433 0 5.00e-01\n 63 1 1 5,449 5,449 5,449 0 5.00e-01\n 77 1 1 5,463 5,463 5,463 0 5.00e-01\n 89 1 1 5,475 5,475 5,475 0 5.00e-01\n 99 1 1 5,485 5,485 5,485 0 5.00e-01\n 107 1 1 5,493 5,493 5,493 0 5.00e-01\n 115 1 1 5,501 5,501 5,501 0 5.00e-01\n 121 1 1 5,507 5,507 5,507 0 5.00e-01\n 127 1 1 5,513 5,513 5,513 0 5.00e-01\n\nRead depth filter: removed 0 contigs totalling 0 bp\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k027.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k047.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k063.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k077.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k089.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k099.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k107.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k115.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k121.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/001_spades_graph_k127.gfa\nDeleting /galaxy/server/database/jobs_directory/000/141/working/spades_assembly/\n\n\nDetermining graph multiplicity (2025-01-14 13:31:32)\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\n\nCleaning graph (2025-01-14 13:31:32)\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 13 14\nGraph overlaps removed\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 (2025-01-14 13:31:32)\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 (2025-01-14 13:31:32)\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 (2025-01-14 13:31:32)\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 (2025-01-14 13:31:32)\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/000/141/working/miniasm_assembly/all_segments.fasta\n1\t5386\t3\t5158\t+\t1\t5386\t227\t5382\t5155\t5155\t255\tcm:i:1149\n1\t5386\t5163\t5383\t+\t1\t5386\t1\t221\t220\t220\t255\tcm:i:47\nNumber of minimap alignments: 1\n\nSaving to /galaxy/server/database/jobs_directory/000/141/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\nDetermining low score threshold (2025-01-14 13:31:32)\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 (2025-01-14 13:31:32)\n1\t5386\t5\t5161\t+\t1\t5386\t229\t5385\t5156\t5156\t255\tcm:i:959\n1\t5386\t5168\t5384\t+\t1\t5386\t6\t222\t216\t216\t255\tcm:i:39\n\nDone! 1 out of 1 reads aligned\n\n\nAligning reads (2025-01-14 13:31:32)\n1/1: 1 (5386 bp)\nminimap alignments:\n 5,5161,+,1,229,5385\n 5168,5384,+,1,6,222\nReference ranges:\n 1+: 0 - 5386\nRange: 1: 0 - 5386\n common 10-mers: 5464\n line 1: 215 points, score=213.009259 (good)\n line 2: 5153 points, score=5151.000388 (good)\nAll Seqan alignments (time to align = 0.058 s):\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 0 224 5162 5386 + 672 100.00 100.00%\n 1 224 5386 0 5162 + 15486 100.00 100.00%\nFinal alignments:\n Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity\n 1 224 5386 0 5162 + 15486 100.00 100.00%\n 1 0 224 5162 5386 + 672 100.00 100.00%\n\n\nRead alignment summary (2025-01-14 13:31:32)\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/000/141/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 (2025-01-14 13:31:32)\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 (2025-01-14 13:31:32)\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\n\nCleaning up leftover segments (2025-01-14 13:31:32)\nSegments eligible for deletion:\n\n\nBridged assembly graph (2025-01-14 13:31:32)\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\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 (2025-01-14 13:31:32)\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/python3.12/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 (2025-01-14 13:31:41)\nSaving /galaxy/server/database/jobs_directory/000/141/working/assembly.gfa\nSaving /galaxy/server/database/jobs_directory/000/141/working/assembly.fasta\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 minutes", "plugin": "core", "name": "runtime_seconds", "raw_value": "148.0000000"}, {"title": "Job End Time", "value": "2025-01-14 13:31:41", "plugin": "core", "name": "end_epoch", "raw_value": "1736861501.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 13:29:13", "plugin": "core", "name": "start_epoch", "raw_value": "1736861353.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "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": 36.456011056900024, "inputs": {"vcf_input": {"src": "hda", "id": "ee08340074ef1ddf"}}, "job": {"model_class": "Job", "id": "fd73c40f1dc190e7", "state": "ok", "exit_code": 0, "update_time": "2025-01-14T12:59:21.554206", "create_time": "2025-01-14T12:59:00.471222", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0", "history_id": "ddd7b7f231ac291f", "external_id": "gxy-6wj8l", "command_line": "vcfgenotypes '/galaxy/server/database/objects/1/4/9/dataset_1498eb3e-09b9-4d1b-88b0-e00e43dcc584.dat' > '/galaxy/server/database/objects/a/5/7/dataset_a574867e-087e-46d0-a4eb-ada76bb39aaa.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"vcf_input": {"id": "ee08340074ef1ddf", "src": "hda", "uuid": "1498eb3e-09b9-4d1b-88b0-e00e43dcc584"}}, "outputs": {"out_file1": {"id": "fd73c40f1dc190e7", "src": "hda", "uuid": "a574867e-087e-46d0-a4eb-ada76bb39aaa"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2025-01-14 12:59:10", "plugin": "core", "name": "start_epoch", "raw_value": "1736859550.0000000"}, {"title": "Job End Time", "value": "2025-01-14 12:59:10", "plugin": "core", "name": "end_epoch", "raw_value": "1736859550.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}], "galaxy_url": "http://35.196.60.149:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.xunit b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.xunit new file mode 100644 index 000000000..a82bf9eca --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.xunit @@ -0,0 +1,868 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + >>STAGE: configure[2025-01-14 13:00:18] INFO: Configuring run[2025-01-14 13:00:18] INFO: Total read length: 7249289[2025-01-14 13:00:18] INFO: Reads N50/N90: 11150 / 5790[2025-01-14 13:00:18] INFO: Minimum overlap set to 6000[2025-01-14 13:00:18] INFO: >>>STAGE: assembly[2025-01-14 13:00:18] INFO: Assembling disjointigs[2025-01-14 13:00:18] INFO: Reading sequences[2025-01-14 13:00:23] INFO: Counting k-mers:0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:01:14] INFO: Filling index table (1/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:01:14] INFO: Filling index table (2/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:01:16] INFO: Extending reads[2025-01-14 13:01:19] INFO: Overlap-based coverage: 10[2025-01-14 13:01:19] INFO: Median overlap divergence: 0.2355840% 80% 90% 100% [2025-01-14 13:01:19] INFO: Assembled 2 disjointigs[2025-01-14 13:01:19] INFO: Generating sequence0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:01:20] INFO: Filtering contained disjointigs0% 50% 100% [2025-01-14 13:01:20] INFO: Contained seqs: 0[2025-01-14 13:01:20] INFO: >>>STAGE: consensus[2025-01-14 13:01:20] INFO: Running Minimap2[2025-01-14 13:01:21] INFO: Computing consensus[2025-01-14 13:01:26] INFO: Alignment error rate: 0.196790Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/41/tmp/pymp-d5yqrrz6'[2025-01-14 13:01:26] INFO: >>>STAGE: repeat[2025-01-14 13:01:26] INFO: Building and resolving repeat graph[2025-01-14 13:01:26] INFO: Parsing disjointigs[2025-01-14 13:01:26] INFO: Building repeat graph0% 50% 100% [2025-01-14 13:01:27] INFO: Median overlap divergence: 0.0761919[2025-01-14 13:01:27] INFO: Parsing reads[2025-01-14 13:01:27] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:01:28] INFO: Aligned read sequence: 6325338 / 6471580 (0.977402)[2025-01-14 13:01:28] INFO: Median overlap divergence: 0.130431[2025-01-14 13:01:28] INFO: Mean edge coverage: 14[2025-01-14 13:01:28] INFO: Simplifying the graph[2025-01-14 13:01:28] INFO: >>>STAGE: contigger[2025-01-14 13:01:28] INFO: Generating contigs[2025-01-14 13:01:28] INFO: Reading sequences[2025-01-14 13:01:28] INFO: Generated 1 contigs[2025-01-14 13:01:28] INFO: Added 0 scaffold connections[2025-01-14 13:01:28] INFO: >>>STAGE: finalize[2025-01-14 13:01:28] INFO: Assembly statistics:Total length:419793Fragments:1Fragments N50:419793Largest frg:419793Scaffolds:0Mean coverage:14[2025-01-14 13:01:28] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/41/working/out_dir/assembly.fasta + ]]> + + + + + + + + >>STAGE: configure[2025-01-14 13:02:01] INFO: Configuring run[2025-01-14 13:02:01] INFO: Total read length: 1466260[2025-01-14 13:02:01] INFO: Reads N50/N90: 9054 / 4697[2025-01-14 13:02:01] INFO: Minimum overlap set to 5000[2025-01-14 13:02:01] INFO: >>>STAGE: assembly[2025-01-14 13:02:01] INFO: Assembling disjointigs[2025-01-14 13:02:01] INFO: Reading sequences[2025-01-14 13:02:05] INFO: Counting k-mers:0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:02:56] INFO: Filling index table (1/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:02:56] INFO: Filling index table (2/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:03:00] INFO: Extending reads[2025-01-14 13:03:03] INFO: Overlap-based coverage: 42[2025-01-14 13:03:03] INFO: Median overlap divergence: 0.1056170% 90% 100% [2025-01-14 13:03:03] INFO: Assembled 1 disjointigs[2025-01-14 13:03:03] INFO: Generating sequence0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:03:03] INFO: Filtering contained disjointigs0% 100% [2025-01-14 13:03:03] INFO: Contained seqs: 0[2025-01-14 13:03:04] INFO: >>>STAGE: consensus[2025-01-14 13:03:04] INFO: Running Minimap2[2025-01-14 13:03:04] INFO: Computing consensus[2025-01-14 13:03:05] INFO: Alignment error rate: 0.175120Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/43/tmp/pymp-c5kjtoiw'[2025-01-14 13:03:05] INFO: >>>STAGE: repeat[2025-01-14 13:03:05] INFO: Building and resolving repeat graph[2025-01-14 13:03:05] INFO: Parsing disjointigs[2025-01-14 13:03:05] INFO: Building repeat graph0% 100% [2025-01-14 13:03:05] INFO: Median overlap divergence: 0.0151003[2025-01-14 13:03:05] INFO: Parsing reads[2025-01-14 13:03:05] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:03:05] INFO: Aligned read sequence: 1166207 / 1313105 (0.888129)[2025-01-14 13:03:05] INFO: Median overlap divergence: 0.0550349[2025-01-14 13:03:05] INFO: Mean edge coverage: 33[2025-01-14 13:03:05] INFO: Simplifying the graph[2025-01-14 13:03:05] INFO: >>>STAGE: contigger[2025-01-14 13:03:05] INFO: Generating contigs[2025-01-14 13:03:05] INFO: Reading sequences[2025-01-14 13:03:05] INFO: Generated 3 contigs[2025-01-14 13:03:05] INFO: Added 0 scaffold connections[2025-01-14 13:03:05] INFO: >>>STAGE: finalize[2025-01-14 13:03:05] INFO: Assembly statistics:Total length:34929Fragments:3Fragments N50:21816Largest frg:21816Scaffolds:0Mean coverage:34[2025-01-14 13:03:05] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/43/working/out_dir/assembly.fasta + ]]> + + + + + + + + + + + + + + + + >>STAGE: configure[2025-01-14 13:04:21] INFO: Configuring run[2025-01-14 13:04:21] INFO: Total read length: 7249289[2025-01-14 13:04:21] INFO: Reads N50/N90: 11150 / 5790[2025-01-14 13:04:21] INFO: Minimum overlap set to 6000[2025-01-14 13:04:21] INFO: >>>STAGE: assembly[2025-01-14 13:04:21] INFO: Assembling disjointigs[2025-01-14 13:04:21] INFO: Reading sequences[2025-01-14 13:04:25] INFO: Counting k-mers:0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:05:15] INFO: Filling index table (1/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:05:16] INFO: Filling index table (2/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:05:18] INFO: Extending reads[2025-01-14 13:05:21] INFO: Overlap-based coverage: 10[2025-01-14 13:05:21] INFO: Median overlap divergence: 0.2355840% 80% 100% [2025-01-14 13:05:21] INFO: Assembled 1 disjointigs[2025-01-14 13:05:21] INFO: Generating sequence0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:05:21] INFO: Filtering contained disjointigs0% 100% [2025-01-14 13:05:22] INFO: Contained seqs: 0[2025-01-14 13:05:22] INFO: >>>STAGE: consensus[2025-01-14 13:05:22] INFO: Running Minimap2[2025-01-14 13:05:23] INFO: Computing consensus[2025-01-14 13:05:28] INFO: Alignment error rate: 0.195502Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/60/tmp/pymp-ljk24ic5'[2025-01-14 13:05:28] INFO: >>>STAGE: repeat[2025-01-14 13:05:28] INFO: Building and resolving repeat graph[2025-01-14 13:05:28] INFO: Parsing disjointigs[2025-01-14 13:05:28] INFO: Building repeat graph0% 100% [2025-01-14 13:05:29] INFO: Median overlap divergence: 0[2025-01-14 13:05:29] INFO: Parsing reads[2025-01-14 13:05:29] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:05:30] INFO: Aligned read sequence: 6338340 / 6471580 (0.979412)[2025-01-14 13:05:30] INFO: Median overlap divergence: 0.129526[2025-01-14 13:05:30] INFO: Mean edge coverage: 14[2025-01-14 13:05:30] INFO: Simplifying the graph[2025-01-14 13:05:30] INFO: >>>STAGE: contigger[2025-01-14 13:05:30] INFO: Generating contigs[2025-01-14 13:05:30] INFO: Reading sequences[2025-01-14 13:05:30] INFO: Generated 1 contigs[2025-01-14 13:05:30] INFO: Added 0 scaffold connections[2025-01-14 13:05:30] INFO: >>>STAGE: polishing[2025-01-14 13:05:30] INFO: Polishing genome (1/1)[2025-01-14 13:05:30] INFO: Running minimap2[2025-01-14 13:05:31] INFO: Separating alignment into bubblesTraceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/60/tmp/pymp-d5lx4ut5'[2025-01-14 13:05:36] INFO: Alignment error rate: 0.126605[2025-01-14 13:05:36] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/60/tmp/pymp-wh3nas6o'[2025-01-14 13:05:40] INFO: >>>STAGE: finalize[2025-01-14 13:05:40] INFO: Assembly statistics:Total length:418049Fragments:1Fragments N50:418049Largest frg:418049Scaffolds:0Mean coverage:17[2025-01-14 13:05:40] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/60/working/out_dir/assembly.fasta + ]]> + + + + + + + + >>STAGE: configure[2025-01-14 13:06:31] INFO: Configuring run[2025-01-14 13:06:31] INFO: Total read length: 6522170[2025-01-14 13:06:31] INFO: Reads N50/N90: 2706 / 1386[2025-01-14 13:06:31] INFO: Selected minimum overlap: 1000[2025-01-14 13:06:31] INFO: >>>STAGE: assembly[2025-01-14 13:06:31] INFO: Assembling disjointigs[2025-01-14 13:06:31] INFO: Reading sequences[2025-01-14 13:06:31] INFO: Building minimizer index[2025-01-14 13:06:31] INFO: Pre-calculating index storage0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:06:32] INFO: Filling index0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:06:32] INFO: Extending reads[2025-01-14 13:06:35] INFO: Overlap-based coverage: 12[2025-01-14 13:06:35] INFO: Median overlap divergence: 0.01356740% 10% 20% 30% 40% 60% 80% 90% 100% [2025-01-14 13:06:35] INFO: Assembled 10 disjointigs[2025-01-14 13:06:35] INFO: Generating sequence0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:06:35] INFO: Filtering contained disjointigs0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:06:35] INFO: Contained seqs: 0[2025-01-14 13:06:35] INFO: >>>STAGE: consensus[2025-01-14 13:06:35] INFO: Running Minimap2[2025-01-14 13:06:36] INFO: Computing consensus[2025-01-14 13:06:37] INFO: Alignment error rate: 0.018062Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/70/tmp/pymp-_jfywtgl'[2025-01-14 13:06:37] INFO: >>>STAGE: repeat[2025-01-14 13:06:37] INFO: Building and resolving repeat graph[2025-01-14 13:06:37] INFO: Parsing disjointigs[2025-01-14 13:06:37] INFO: Building repeat graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:06:37] INFO: Median overlap divergence: 0.00146056[2025-01-14 13:06:37] INFO: Parsing reads[2025-01-14 13:06:37] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:06:38] INFO: Aligned read sequence: 6385160 / 6522170 (0.978993)[2025-01-14 13:06:38] INFO: Median overlap divergence: 0.00691777[2025-01-14 13:06:38] INFO: Mean edge coverage: 14[2025-01-14 13:06:38] INFO: Simplifying the graph[2025-01-14 13:06:38] INFO: >>>STAGE: contigger[2025-01-14 13:06:38] INFO: Generating contigs[2025-01-14 13:06:38] INFO: Reading sequences[2025-01-14 13:06:38] INFO: Generated 4 contigs[2025-01-14 13:06:38] INFO: Added 0 scaffold connections[2025-01-14 13:06:38] INFO: >>>STAGE: polishing[2025-01-14 13:06:38] INFO: Polishing genome (1/1)[2025-01-14 13:06:38] INFO: Running minimap2[2025-01-14 13:06:38] INFO: Separating alignment into bubblesTraceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/70/tmp/pymp-qrfceht3'[2025-01-14 13:06:40] INFO: Alignment error rate: 0.010378[2025-01-14 13:06:40] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/70/tmp/pymp-bh0w3wrf'[2025-01-14 13:06:42] INFO: >>>STAGE: finalize[2025-01-14 13:06:42] INFO: Assembly statistics:Total length:419248Fragments:4Fragments N50:147965Largest frg:150253Scaffolds:0Mean coverage:16[2025-01-14 13:06:42] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/70/working/out_dir/assembly.fasta + ]]> + + + + + + + + >>STAGE: configure[2025-01-14 13:07:34] INFO: Configuring run[2025-01-14 13:07:34] INFO: Total read length: 6522170[2025-01-14 13:07:34] INFO: Reads N50/N90: 2706 / 1386[2025-01-14 13:07:34] INFO: Selected minimum overlap: 1000[2025-01-14 13:07:34] INFO: >>>STAGE: assembly[2025-01-14 13:07:34] INFO: Assembling disjointigs[2025-01-14 13:07:34] INFO: Reading sequences[2025-01-14 13:07:35] INFO: Building minimizer index[2025-01-14 13:07:35] INFO: Pre-calculating index storage0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:07:35] INFO: Filling index0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:07:35] INFO: Extending reads[2025-01-14 13:07:38] INFO: Overlap-based coverage: 12[2025-01-14 13:07:38] INFO: Median overlap divergence: 0.01356740% 10% 20% 30% 40% 60% 80% 90% 100% [2025-01-14 13:07:38] INFO: Assembled 12 disjointigs[2025-01-14 13:07:38] INFO: Generating sequence0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:07:38] INFO: Filtering contained disjointigs0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:07:38] INFO: Contained seqs: 0[2025-01-14 13:07:38] INFO: >>>STAGE: consensus[2025-01-14 13:07:38] INFO: Running Minimap2[2025-01-14 13:07:39] INFO: Computing consensus[2025-01-14 13:07:40] INFO: Alignment error rate: 0.018150Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/80/tmp/pymp-pnh8pejn'[2025-01-14 13:07:40] INFO: >>>STAGE: repeat[2025-01-14 13:07:40] INFO: Building and resolving repeat graph[2025-01-14 13:07:40] INFO: Parsing disjointigs[2025-01-14 13:07:40] INFO: Building repeat graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:07:40] INFO: Median overlap divergence: 0.00293725[2025-01-14 13:07:40] INFO: Parsing reads[2025-01-14 13:07:40] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:07:41] INFO: Aligned read sequence: 6400847 / 6522170 (0.981398)[2025-01-14 13:07:41] INFO: Median overlap divergence: 0.00690788[2025-01-14 13:07:41] INFO: Mean edge coverage: 14[2025-01-14 13:07:41] INFO: Simplifying the graph[2025-01-14 13:07:41] INFO: >>>STAGE: contigger[2025-01-14 13:07:41] INFO: Generating contigs[2025-01-14 13:07:41] INFO: Reading sequences[2025-01-14 13:07:41] INFO: Generated 5 contigs[2025-01-14 13:07:41] INFO: Added 0 scaffold connections[2025-01-14 13:07:41] INFO: >>>STAGE: polishing[2025-01-14 13:07:41] INFO: Polishing genome (1/1)[2025-01-14 13:07:41] INFO: Running minimap2[2025-01-14 13:07:42] INFO: Separating alignment into bubblesTraceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/80/tmp/pymp-e8n043xf'[2025-01-14 13:07:43] INFO: Alignment error rate: 0.009940[2025-01-14 13:07:43] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/80/tmp/pymp-yuvrjvx1'[2025-01-14 13:07:50] INFO: >>>STAGE: finalize[2025-01-14 13:07:50] INFO: Assembly statistics:Total length:418250Fragments:5Fragments N50:90295Largest frg:147965Scaffolds:0Mean coverage:16[2025-01-14 13:07:50] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/80/working/out_dir/assembly.fasta + ]]> + + + + + + + + + + + + + + >>STAGE: configure[2025-01-14 13:09:15] INFO: Configuring run[2025-01-14 13:09:15] INFO: Total read length: 6522170[2025-01-14 13:09:15] INFO: Reads N50/N90: 2706 / 1386[2025-01-14 13:09:15] INFO: Selected minimum overlap: 1000[2025-01-14 13:09:15] INFO: >>>STAGE: assembly[2025-01-14 13:09:15] INFO: Assembling disjointigs[2025-01-14 13:09:15] INFO: Reading sequences[2025-01-14 13:09:15] INFO: Building minimizer index[2025-01-14 13:09:15] INFO: Pre-calculating index storage0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:09:16] INFO: Filling index0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:09:16] INFO: Extending reads[2025-01-14 13:09:19] INFO: Overlap-based coverage: 12[2025-01-14 13:09:19] INFO: Median overlap divergence: 0.01356740% 10% 20% 30% 40% 70% 80% 90% 100% [2025-01-14 13:09:19] INFO: Assembled 11 disjointigs[2025-01-14 13:09:19] INFO: Generating sequence0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:09:19] INFO: Filtering contained disjointigs0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:09:19] INFO: Contained seqs: 0[2025-01-14 13:09:19] INFO: >>>STAGE: consensus[2025-01-14 13:09:19] INFO: Running Minimap2[2025-01-14 13:09:20] INFO: Computing consensus[2025-01-14 13:09:21] INFO: Alignment error rate: 0.018082Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/99/tmp/pymp-n2s5mmme'[2025-01-14 13:09:21] INFO: >>>STAGE: repeat[2025-01-14 13:09:21] INFO: Building and resolving repeat graph[2025-01-14 13:09:21] INFO: Parsing disjointigs[2025-01-14 13:09:21] INFO: Building repeat graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:09:21] INFO: Median overlap divergence: 0.000980392[2025-01-14 13:09:21] INFO: Parsing reads[2025-01-14 13:09:21] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:09:22] INFO: Aligned read sequence: 6403986 / 6522170 (0.98188)[2025-01-14 13:09:22] INFO: Median overlap divergence: 0.00689656[2025-01-14 13:09:22] INFO: Mean edge coverage: 14[2025-01-14 13:09:22] INFO: Simplifying the graph[2025-01-14 13:09:22] INFO: >>>STAGE: contigger[2025-01-14 13:09:22] INFO: Generating contigs[2025-01-14 13:09:22] INFO: Reading sequences[2025-01-14 13:09:22] INFO: Generated 4 contigs[2025-01-14 13:09:22] INFO: Added 0 scaffold connections[2025-01-14 13:09:22] INFO: >>>STAGE: polishing[2025-01-14 13:09:22] INFO: Polishing genome (1/1)[2025-01-14 13:09:22] INFO: Running minimap2[2025-01-14 13:09:22] INFO: Separating alignment into bubblesTraceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/99/tmp/pymp-5kmiqtfe'[2025-01-14 13:09:24] INFO: Alignment error rate: 0.009628[2025-01-14 13:09:24] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/99/tmp/pymp-0620o1k5'[2025-01-14 13:09:26] INFO: >>>STAGE: finalize[2025-01-14 13:09:26] INFO: Assembly statistics:Total length:419247Fragments:4Fragments N50:147964Largest frg:150253Scaffolds:0Mean coverage:16[2025-01-14 13:09:26] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/99/working/out_dir/assembly.fasta + ]]> + + + + + + + + >>STAGE: configure[2025-01-14 13:09:55] INFO: Configuring run[2025-01-14 13:09:55] INFO: Total read length: 1466260[2025-01-14 13:09:55] INFO: Reads N50/N90: 9054 / 4697[2025-01-14 13:09:55] INFO: Minimum overlap set to 5000[2025-01-14 13:09:55] INFO: >>>STAGE: assembly[2025-01-14 13:09:55] INFO: Assembling disjointigs[2025-01-14 13:09:55] INFO: Reading sequences[2025-01-14 13:10:00] INFO: Counting k-mers:0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:10:51] INFO: Filling index table (1/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:10:51] INFO: Filling index table (2/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:10:55] INFO: Extending reads[2025-01-14 13:10:58] INFO: Overlap-based coverage: 42[2025-01-14 13:10:58] INFO: Median overlap divergence: 0.1056170% 90% 100% [2025-01-14 13:10:58] INFO: Assembled 1 disjointigs[2025-01-14 13:10:58] INFO: Generating sequence0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:10:58] INFO: Filtering contained disjointigs0% 100% [2025-01-14 13:10:58] INFO: Contained seqs: 0[2025-01-14 13:10:58] INFO: >>>STAGE: consensus[2025-01-14 13:10:58] INFO: Running Minimap2[2025-01-14 13:10:58] INFO: Computing consensus[2025-01-14 13:10:59] INFO: Alignment error rate: 0.175120Traceback (most recent call last): File "/usr/local/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 599, in _run_server server.serve_forever() File "/usr/local/lib/python3.12/multiprocessing/managers.py", line 184, 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/python3.12/multiprocessing/util.py", line 303, in _run_finalizers finalizer() File "/usr/local/lib/python3.12/multiprocessing/util.py", line 227, in __call__ res = self._callback(*self._args, **self._kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/multiprocessing/util.py", line 136, in _remove_temp_dir rmtree(tempdir, onerror=onerror) File "/usr/local/lib/python3.12/shutil.py", line 759, in rmtree _rmtree_safe_fd(stack, onexc) File "/usr/local/lib/python3.12/shutil.py", line 703, in _rmtree_safe_fd onexc(func, path, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 700, in _rmtree_safe_fd onexc(os.unlink, fullname, err) File "/usr/local/lib/python3.12/shutil.py", line 750, in onexc return onerror(func, path, exc_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/shutil.py", line 698, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '/galaxy/server/database/jobs_directory/000/101/tmp/pymp-fr22sh1t'[2025-01-14 13:10:59] INFO: >>>STAGE: repeat[2025-01-14 13:10:59] INFO: Building and resolving repeat graph[2025-01-14 13:10:59] INFO: Parsing disjointigs[2025-01-14 13:10:59] INFO: Building repeat graph0% 100% [2025-01-14 13:11:00] INFO: Median overlap divergence: 0.0151003[2025-01-14 13:11:00] INFO: Parsing reads[2025-01-14 13:11:00] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2025-01-14 13:11:00] INFO: Aligned read sequence: 1166207 / 1313105 (0.888129)[2025-01-14 13:11:00] INFO: Median overlap divergence: 0.0550349[2025-01-14 13:11:00] INFO: Mean edge coverage: 33[2025-01-14 13:11:00] INFO: Simplifying the graph[2025-01-14 13:11:00] INFO: >>>STAGE: contigger[2025-01-14 13:11:00] INFO: Generating contigs[2025-01-14 13:11:00] INFO: Reading sequences[2025-01-14 13:11:00] INFO: Generated 1 contigs[2025-01-14 13:11:00] INFO: Added 0 scaffold connections[2025-01-14 13:11:00] INFO: >>>STAGE: finalize[2025-01-14 13:11:00] INFO: Assembly statistics:Total length:5027Fragments:1Fragments N50:5027Largest frg:5027Scaffolds:0Mean coverage:95[2025-01-14 13:11:00] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/101/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 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 ResultCleaning up leftover segments (2025-01-14 13:18:22)Segments eligible for deletion:Bridged assembly graph (2025-01-14 13:18:22) 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.Component Segments Links Length N50 Longest segment Status 1 1 1 5,386 5,386 5,386 completeRotating completed replicons (2025-01-14 13:18:22) 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/python3.12/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 (2025-01-14 13:18:31)Saving /galaxy/server/database/jobs_directory/000/118/working/assembly.gfaSaving /galaxy/server/database/jobs_directory/000/118/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 (2025-01-14 13:21:22) 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 (2025-01-14 13:21:22)1538655161+15386229538551565156255cm:i:9591538651685384+153866222216216255cm:i:39Done! 1 out of 1 reads alignedAligning reads (2025-01-14 13:21:22)1/1: 1 (5386 bp)minimap alignments: 5,5161,+,1,229,5385 5168,5384,+,1,6,222Reference ranges: 1+: 0 - 5386Range: 1: 0 - 5386 common 10-mers: 5464 line 1: 215 points, score=213.009259 (good) line 2: 5153 points, score=5151.000388 (good)All Seqan alignments (time to align = 0.058 s): Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity 1 0 224 5162 5386 + 672 100.00 100.00% 1 224 5386 0 5162 + 15486 100.00 100.00%Final alignments: Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity 1 224 5386 0 5162 + 15486 100.00 100.00% 1 0 224 5162 5386 + 672 100.00 100.00%Read alignment summary (2025-01-14 13:21:22)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/000/122/working/read_alignment/Setting the minimum scaled score to the 5.0th percentile of full read alignments: 0.00Building long read bridges (2025-01-14 13:21:22) 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 (2025-01-14 13:21:22) 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 ResultCleaning up leftover segments (2025-01-14 13:21:22)Segments eligible for deletion:Bridged assembly graph (2025-01-14 13:21:22) 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.Component Segments Links Length N50 Longest segment Status 1 1 1 5,386 5,386 5,386 completeRotating completed replicons (2025-01-14 13:21:22) 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/python3.12/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 (2025-01-14 13:21:31)Saving /galaxy/server/database/jobs_directory/000/122/working/assembly.gfaSaving /galaxy/server/database/jobs_directory/000/122/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/000/126/working/miniasm_assembly/12_unitig_graph.gfaPolishing miniasm assembly with Racon (2025-01-14 13:22:21) 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/000/126/working/miniasm_assembly/racon_polish/polishing_reads.fastq: 40 long readsPolish Assembly Mappinground size quality0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template42862104010+158361061460311473800255cm:i:2000237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template4286129722+1583652215833179612255cm:i:27054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template44139344391-158362376583334573457255cm:i:1153054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template44131262525-158363023147872399255cm:i:1443708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template46052804284-158364393614814004255cm:i:2463708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template460527194286-15836421558335461618255cm:i:884850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template41271704027+158361680583310324153255cm:i:1744850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template412728934082+15836416022201598255cm:i:30598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template458713344566-158362699578612813232255cm:i:243598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template4587982778-158365026637722680255cm:i:129771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template461512254611-158362657583314693386255cm:i:268771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template4615972786-158363026369052689255cm:i:1579780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template43331434271-15836338425418344128255cm:i:4709780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template433330924330-15836450357984301295255cm:i:779e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template45365444408-1583669392712083864255cm:i:2379e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template453630084472-15836421557483511533255cm:i:53a152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template433106396+1583629093222131313255cm:i:22a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template44563354397+158361321525713514062255cm:i:280a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template445634374349+1583623961238938255cm:i:40a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template445686537+1583653345798154464255cm:i:26b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template44351114359-158361673579820624248255cm:i:487b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template44351091619-158363015254721510255cm:i:68bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template4275934048+158361733583313034100255cm:i:230bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template427525324244+15836416903111712255cm:i:43f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template45092894205+1583623393910393916255cm:i:166f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template45092961782+15836424257983671556255cm:i:63begin 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7.820237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template42861294010+162421016500924603993255cm:i:5300237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template4286129722+1624256266239283613255cm:i:610237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template428636324010+162424408117404255cm:i:18054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template44139344391-162422535623922343704255cm:i:514054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template44131262508-1624251246913872418255cm:i:2713708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template46051104284-162424427623804272255cm:i:4943708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template460527194590-16242431462399551925255cm:i:1964850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template41271084027+162421759623921944480255cm:i:4404850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template412728934124+16242417354501731255cm:i:67598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template458713454580-162422848617822843330255cm:i:509598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template4587982778-1624251282515042774255cm:i:295771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template461512254611-162422819623922353420255cm:i:510771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template46151092745-1624274278715172713255cm:i:3049780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template43331404284-16242358465920514301255cm:i:3919780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template433330694304-16242493962236181284255cm:i:1149e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template45361384408-1624272449319414421255cm:i:3459e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template453630024533-16242455661585791602255cm:i:105a152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template433106396+1624230773380169303255cm:i:32a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template4456864397+162421133566424054531255cm:i:507a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template445634374397+162422310513531028255cm:i:59a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template4456107539+1624257596206204447255cm:i:40b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template44351054374-162421799621027494411255cm:i:591b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template44351051578-162427416017951527255cm:i:165bca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template1421122847+1624251665916224750255cm:i:35bca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template1421160847+162426021310144708255cm:i:16bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template42751244048+162421908623920614331255cm:i:454bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template427525324244+16242418316671827255cm:i:111c2f682b3-3774-41a5-8663-32d081b558ee_Basecall_1D_template114897391+1624220532352157299255cm:i:37f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template45092894485+1624223439521304372255cm:i:425f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template45091111803+16242444762257621778255cm:i:1382 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6,265 8.04Best polish: /galaxy/server/database/jobs_directory/000/126/working/miniasm_assembly/racon_polish/016_rotated.fastaSaving /galaxy/server/database/jobs_directory/000/126/working/miniasm_assembly/13_racon_polished.gfaAssembly complete (2025-01-14 13:22:22)Saving /galaxy/server/database/jobs_directory/000/126/working/assembly.gfa + ]]> + + + + + + + + + + + + + + end Path Quality ResultSaving /galaxy/server/database/jobs_directory/000/133/working/004_bridges_applied.gfaCleaning up leftover segments (2025-01-14 13:25:32)Segments eligible for deletion:Bridged assembly graph (2025-01-14 13:25:32) 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/000/133/working/005_final_clean.gfaComponent Segments Links Length N50 Longest segment Status 1 1 1 5,386 5,386 5,386 completeRotating completed replicons (2025-01-14 13:25:32) 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/python3.12/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 (2025-01-14 13:25:41)Saving /galaxy/server/database/jobs_directory/000/133/working/assembly.gfaSaving /galaxy/server/database/jobs_directory/000/133/working/assembly.fasta + ]]> + + + + + + + + + + + + + + + + + + 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 (2025-01-14 13:31:32) 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 ResultCleaning up leftover segments (2025-01-14 13:31:32)Segments eligible for deletion:Bridged assembly graph (2025-01-14 13:31:32) 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.Component Segments Links Length N50 Longest segment Status 1 1 1 5,386 5,386 5,386 completeRotating completed replicons (2025-01-14 13:31:32) 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/python3.12/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 (2025-01-14 13:31:41)Saving /galaxy/server/database/jobs_directory/000/141/working/assembly.gfaSaving /galaxy/server/database/jobs_directory/000/141/working/assembly.fasta + ]]> + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/tools.yml b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/tools.yml new file mode 100644 index 000000000..e11edc665 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/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: toolshed.g2.bx.psu.edu +- name: reshape2_melt + owner: iuc + revisions: + - 317ed0ee8bf2 + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fasta_compute_length + owner: devteam + revisions: + - 7d37cfda8e00 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bamtools + owner: devteam + revisions: + - 4d343c1f606b + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: samtools_idxstats + owner: devteam + revisions: + - 7a6034296ae9 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bcftools_gtcheck + owner: iuc + revisions: + - 672b6c02fbc7 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bcftools_reheader + owner: iuc + revisions: + - 9ef52d95114b + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bcftools_plugin_tag2tag + owner: iuc + revisions: + - bdfdf5f6e950 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfgenotypes + owner: devteam + revisions: + - a60ae8af21a1 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: flye + owner: bgruening + revisions: + - 3ee0ef312022 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: poretools_tabular + owner: iuc + revisions: + - 2cb2feb94f0e + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: deeptools_multi_bigwig_summary + owner: bgruening + revisions: + - 3c9f0c486cca + tool_panel_section_label: deepTools + tool_shed_url: toolshed.g2.bx.psu.edu +- name: unicycler + owner: iuc + revisions: + - 9e3e80cc4ad4 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ivar_removereads + owner: iuc + revisions: + - ee2beb764a7b + tool_panel_section_label: Virology + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hisat2 + owner: iuc + revisions: + - 26371a1df031 + tool_panel_section_label: RNA-seq + tool_shed_url: toolshed.g2.bx.psu.edu